Here is how I explain the difference in the aliens and the time between Crysis1 and Crysis2

A long, long time ago in a galaxy far, far away...(LOL)
Here it goes: (Spoiler)
The aliens that we see in NY are the original colonists of earth that came here billion of years ago.
They arrived on earth to colonise it and for the natural resources, at that time we had only the one continent and the rest of the planet was covered by oceans so it seemed like a perfect planet to start a colony on.
This earth CEPH adapted to the gravity of earth over years and years, creating bipedal suits and becoming more tolerable to earth's environment.
They had both contact and exchange of resources and technology with the home planet over those years.
One day a great cataclysm hit the earth very suddenly not allowing even a distress call to be sent, a polar shift which caused the single continent to break up and to start drifting, eventually forming the earth as we know it today.
At the time of the cataclysm the earth CEPH suffered great losses in numbers and the remainder of the survivors was forced to go deep in to the ocean for protection, unfortunately the safety they found also became their prison, trapping them at the bottom of the ocean. To survive they decided to go into a hibernating state.
After a while and no communication from earth the CEPH decided to send out scouting party to find out what happened to the earth CEPH.
After some time the CEPH scouting party came to earth and found a strange new world nothing like they were told about, there was also no sign of the earth CEPH.
On returning home and informing them of the strange world they have found the CEPH decided to prepare a secondary expedition force to retake the planet and find out what happened to the earth CEPH. This took time but a expedition finally left the CEPH home planet for earth.
As they were approaching earth they were hit by a solar flare, knocking out and draining their power causing the ship to crash on an island.
At that time the earth was suffering from asteroid strikes and was enveloped in a nuclear winter.
Having no sun as a source of power and having limited power themselves, they then sent out scouts to survey the land and to see if they can find any source of power that they can use to repower the ship, unfortunately there was none and so with that they sent out a signal back home saying: "Don't come for us, earth is unstable for colonization , await our awakening when things calm down."
The whole expedition went into hibernation, including the scouts that where now all around the world.
Years past and the ship was covered by sand and eventually was cocooned in the earth not receiving any light for millennia.
Eventually humans came to what we know them today and as the climate changed the earth CEPH where released from their prison (due to earthquakes and continues continental shift) as they came up to the surface they found a new dominant lifeform on earth, us. As any intelligent species they first wanted to study us and to find out our weaknesses before attacking us and so they created in secret cells all over the world to observe and study us.
In the mean time humans found the fossil remains of some of the scouts that were forced to power down from the second expedition force (Tunguska incident)
Couple years past and some technology emerged from the research of the stolen alien technology like the nanosuit.
A second site was found with fossils on an island in the Pacific. Hargreave decides to send Prophet with a team of special forces "to get the researches out", in reality they were sent as test subject. (Crysis 1 starts)
When the fighting awakes the expedition force of CEPH they start to drain power from the humans and start to wake each other up. eventually the nuke gives them enough power and they link up with all the cells on earth (earth CEPHs).
During their fighting they send out a signal to home world informing them of what has happened, and the new threat.
After Prophet returns to the island by borrowing the ship, he discovers the more information about the CEPH and decides to go back to Hargreave to report.
He then leaves Nomad and Psycho to carry on fighting as he goes back to inform Hargreave about what he found.
He removes his suit for the journey back home.
Due to amount of time spent in the suits without taking them of the special forces personal become walking dead man, if they remove the suits they will start to die, unfortunately they don't know that and Prophet starts to get sick on the journey back.
On his arrival at Hargreave he is placed in V2 Nanosuit to save his life and he is told the truth (Video where he gets pissed off) He is then told to go back which he does and discovers the cells all over the world. (Not sure from the vids but to me it seemed that he got teleported back into NY cell from the island...) Since he was one of the first to come into contact with the CEPH at NY before they came out of hiding he gets contaminated there. He returns again to Hargreave and they start with their testing of the virus. At that time earth CEPH already started to spread the virus.
At the same time as Crysis1 happens the earth CEPH decide that time is now to strike as they have found a biological agent to kill humans. They slowly start to release the agent first for testing and then full scale for invasion purposes. (Crysis2 begins)
At some point Prophet gets in touch with Gould and they both decide to try and stop the CEPH as Hargreave is mad. Crysis2

As I see it then you can have up to 3 different CEPH.
Earth CEPH evolved on earth(Crysis2)
Exploration CEPH (Crysis1)
Main CEPH (can have even more different technology as they developed during the hibernation of the first two CEPH factions)
This is my explanation to myself to fill in the holes in the story as best as I can, it is not perfect what you guys think?

aliens from Crysis 1 were here for millions of years, they sent distress signal to CEPH who came here form their planet which is very far away, thats why it took 3 years for them to come. So Crysis 1 aliens wanted our planet cuz it had water but they crashed and now we awakened them they are going take what is theirs. Cuz they were here first.....
N1 was took weak against the plague or whatever it was and he got infected, N2 kept him alive a bit longer but he was **** anyway
Basically nothing happened between crysis 1 and 2 cuz the CEPH were flying in space and Prophet was hiding from CELL cuz he didn't trust them

aliens from Crysis 1 were here for millions of years, they sent distress signal to CEPH who came here form their planet which is very far away, thats why it took 3 years for them to come. So Crysis 1 aliens wanted our planet cuz it had water but they crashed and now we awakened them they are going take what is theirs. Cuz they were here first.....
N1 was took weak against the plague or whatever it was and he got infected, N2 kept him alive a bit longer but he was **** anyway
Basically nothing happened between crysis 1 and 2 cuz the CEPH were flying in space and Prophet was hiding from CELL cuz he didn't trust them

Few things though.
1. Prophet stated in one of the Vids they were here all along.
2. Hargreave said they evolved in the oceans.
3. If they travelled in 3 years from their planet. When did they set up cells all over the world. They must have received the full human genome in the message, they had to create the virus with no test subjects and hope it works when they arrived on earth.
Unless of course you are saying that they received the message, built up an invasion force, travelled to earth, decided on strategic points to land, landed and created the virus within only 3 years.
4. No one noticed them landing in central park or anywhere else in the world?
5. How can a race that crashed and went into hibernation suddenly be thought of as the owners of the planet by Hargreave? Unless they evacuated back into a crashed ship and went into hibernation for some reason.
I'm sorry but it leaves to many questions and more holes for me.
Personally I think the main invasion force is still coming.

if you did not notice, nano suit 2 was on prophet when he go through the gate to new york, this is why hargreave want the suit so bad. the suit from crysis 1 adapt with the alien tech and form suit 2. and so that become the only nano suit 2.0 on the planet. if hargraeve invented suit 2.0 dont you think he would already wear it? no, hargreave already want the suit even before he gave it to alcatraz which give additional alien tech to the suit through tissue. and if i remember right, it did state in one of the ingame video.

if you did not notice, nano suit 2 was on prophet when he go through the gate to new york, this is why hargreave want the suit so bad. the suit from crysis 1 adapt with the alien tech and form suit 2. and so that become the only nano suit 2.0 on the planet. if hargraeve invented suit 2.0 dont you think he would already wear it? no, hargreave already want the suit even before he gave it to alcatraz which give additional alien tech to the suit through tissue. and if i remember right, it did state in one of the ingame video.
If you visit crynet http://www.crynetsystems.com/ then it shows vids and brochure for the Nanaosuit2, so crynet did create it as far as I know.
Spoiler: The only reason why Hargraeve wanted the suit is because of the CEPH virus code inside it. He didn't want to have Nanosuit 2 for the sake of wearing it he wanted to destroy the CEPH with that specific one. He thought he is the only one that can and should do it as he woke them up.

Few things though.
1. Prophet stated in one of the Vids they were here all along.
2. Hargreave said they evolved in the oceans.
3. If they travelled in 3 years from their planet. When did they set up cells all over the world. They must have received the full human genome in the message, they had to create the virus with no test subjects and hope it works when they arrived on earth.
Unless of course you are saying that they received the message, built up an invasion force, travelled to earth, decided on strategic points to land, landed and created the virus within only 3 years.
4. No one noticed them landing in central park or anywhere else in the world?
5. How can a race that crashed and went into hibernation suddenly be thought of as the owners of the planet by Hargreave? Unless they evacuated back into a crashed ship and went into hibernation for some reason.
I'm sorry but it leaves to many questions and more holes for me.
Personally I think the main invasion force is still coming.

1. they were, the aliens in crysis 1 were here for 2 million years
2. they did, so we know their planet contains a lot of water and they didnt have gravity in alien ship in crysis 1
3. im confused with these underground things too and they are a bit ahead of us in technology so maybe they could have created the plague. It is said in the book that maybe they were testing the plague because NY area was the only place where there was plague
4. and 5. well Crysis 2 is a reboot so maybe earth was their planet but then something happened

If this wasn't main invasion force then there is no point fighting cuz they are kicking our asses and we only have 1 guy in a nanosuit. and we are fighting each other too....

Cool story bro.

“The spore might not be a bioweapon after all,” Gould continues. “At least, not just a bioweapon, not the way we’d understand it. If these readings are right it might almost be a kind of, of portable ecosystem. No, scratch that: more of an external immune system. It basically retcons the local environment to make it Ceph-friendly. That means taking out potentially dangerous macrofauna, of course—”
“Us, you mean,” Barclay murmurs.
“—but I think it also filters out any microbes that might be incompatible with Ceph biology.”

So this Spore is something they unleash on every planet and see how it goes....

You mean, something like nanites. They get into a hostile life form, aka us, and find the best way to neutralise the hostile life form.
The spores created a sense of euphoria while killing the person inside, so there was no fighting or screaming, etc
Genius idea that. The nanosuit might be even based from that tech.

LOL would be funny if everybody gets together and we all write a story for Crytek and they actually use it

Cool story bro.
Thank you