So to build off ideas posted here http://www.gamesas.com/topic/1540164-endgame-suggestion-faction-warning-long-text/ I would like to add in my own suggestions to this.
200 Dweller content
There are no rooms for anything after 100 Dwellers. For those who seek to maximize their vaults. Here's what could be added.
120 - Trading Post: The ability to turn in excess resources for other resources your lacking. (ex. Trading 100 Water for 100 Power)
140 - Clothier: (using dwellers with stats of Intelligence and Perception) The ability to create a piece of randomized clothing once every real time hour.
160 - Workbench: (using dwellers with stats of Strength and Endurance) The ability to create a piece of randomized weaponry once every real time hour.
180 - Newspaper: (using dwellers with stats of Charisma and Luck) The ability to attract a higher stat dwellers once every real time hour.
200 - Bio-Dome: (using dwellers with Agility and Perception) The ability to create all three resources in one room.
Instances
Lets say once every 5 hours a dweller is in the wasteland (or a randomized time) You get the ability to send him into an Instance. In these Instances (similar to the missions in the linked post) dwellers can enter into random areas (caves, other vaults, buildings, etc.) and enter into a turn based firefight. They can use abilities (or perks) granted to them by whatever level stat they are. Example. A dweller with a strength of 5 can melee, a dweller with a agility of 6 can use V.A.T.S. for a critical. In these Instances, when its your turn you can use these abilities to win and get a increased chance at higher tier loot.
Or institute this as a daily challenge. once every 24 hours, you get into an Instance using a dweller of your choosing. Send them into a turn based combat situation. Use abilities at a chance to either get a random high level gun. At the end of the week, you get a big firefight where you can send 3 dwellers into battle with a chance to get a free premium lunchbox (a chance to get a Mr. Handy or guaranteed high tier weapon).
If these were implemented it would turn this either into Pokémon or early final fantasy type of battle.
New Enemy Invasions
So far there are only raiders and deathclaws that hammer down the door and attack your vault. On a regular vault (no survival mode) most of the time, they barely make it past the first couple of levels (if your good at the game they barely make it out of the vault door room). So lets add new enemies.
Super Mutants: Lets give them as much health as the Deathclaws, but they use randomized guns (example: hunting rifle does what 5 damage). Lets do 2 of them attack until 100 dwellers and 4 attack at 200 dwellers.
Mirelurks: Lets give them medium health (somewhere between raiders and deathclaws). Lets do 3 of them at 100 dwellers and 6 at 200 dwellers.
Raider Leaders: Give them as much health as mirelurks. Do 3 of them at 100 dwellers and 6 at 200. with randomized guns.
*UPDATED 10/26
Geckos: Medium health, attacks in 3-4 of them. starts attacking around 50 dwellers.
New Game Mechanics
New mechanics would be good to implement.
Ability to Sell Stimpacks and Radaways: Allows for selling of stimpack and radaways at maybe 50 caps a pop.
Daily Slot Machine: Allows for a daily chance at either some free resources, or stimpacks, radaways, guns, outfits, or caps.
Incidents
Adding in a few more incidents that are random would make this game feel alittle bit more fallout. Activated when rooms are rushed.
Radiation (or Gas) Leak: The room gets flooded with radiation, all dwellers flee (or die if you don't move them) for a random amount of time up to no more than a minute.
Flood: The room gets flooded with water, all dwellers flee (or die if you don't move them) for a random amount of time.
Bug Attack: Bloatfly,Bloodsvckers, or Mantis's come out of the ground and attack until killed.
Rockslide: Rocks come tumbling down from above hurting dwellers, and then they have to move them to end the incident.
Other
This section is for other ideas that just didn't match a section above.
Experiment Room: In living with the original sense that vaults were experiments. Add in an experiment room that can be accessed at 25 dwellers. In this room you can either activate a random incident without the need to rush. This can use up lets say 25 power.
Vault Door Room Upgrade 3: Vault door gets more health (to withstand bigger enemies) as well as 2 laser turrets are added.
Security Stations: (dwellers with strength) mans turrets against enemies. access at 55 dwellers. 3 Upgrades, 1st upgrade is single shot turrets, 2nd upgrade are chainguns, 3rd upgrade are laser gattling guns. (triple room max, 2 dwellers only per room, 2 turrets per room max)
Sacrificial Room: build at 75 dwellers, the ability to kill off specific dwellers so you can either gain a new dweller (if you've maxed out your population before building new living quarters).
Hospital: build at 25 dwellers, the ability to resurrect a dweller without the need for caps. once per 30 minutes. (dwellers with Intelligence, perception, and luck). Cannot build in survival mode.
* Updated 10/22
Cap Sinks
Things to buy towards endgame that cost a lot of caps.
$100,000 caps: Extra Randomized Resources
$200,000 caps: 1 Randomized Stat Dweller
$300,000 caps: Auto-Collect Resource Rooms
$400,000 caps: Auto-Collect Stat Builder Rooms
$500,000 caps: 1 Randomized Blue or higher Outfit
$600,000 caps: 1 Randomized Blue or higher Weapon
$700,000 caps: Happiness Boost (an hour or two long boost that heightens happiness)
$800,000 caps: Time Boost (an hour or two long boost that speeds up resource production)
$900,000 caps: 1 Mr. Handy lunchbox
$999,999 caps: 1 free lunchbox
* Updated 10/26
Pets
These would be able to be added through either a random chance in the wasteland, radio calling, or lunchbox. All can attack any attackers entering the vault.
Dogmeat: raises the happiness of the dwellers in the rooms he enters. can go into the wasteland to collect caps, outfits, and weapons. can go through the entire vault, using elevators. can also gain levels.
R.O.U.S. (Rats of Unusual Size): collects random amounts of "lose caps" that have fallen on the floor by vault dwellers. 10-25 caps generated per 10 minutes.
Stripe (mini Deathclaw from FO:NV): has strong health. can patrol the entire vault and gain levels. can also be revived as well.
RoboBrain: Patrols a single level of the vault. has stronger health than Mr. Handy. Cannot help with incidents, just attackers and cannot auto collect resources.
Securitron: can only patrol the top most level of the vault. can help with incidents and attacks but not collect resources.
Protectron: can do everything a Mr. Handy can, has higher health, and can travel the entire vault. just really slowly.
Sentry Bot: Can only be placed in the Vault Door room. has high health and strong weapons. attacks intruders and can go collect caps, weapons and outfits from the wasteland.
**** Update:
Pets: Would like to mention that I had posted this suggestion on 10/15/2015, long before they added pets to the game. Maybe they liked the suggestion. who knows.
I know some of my ideas are good. However, doing things like Daily and Weekly things would require this game to have a connection.... but it could still be set up that if there is no connection it just doesn't activate the mechanic. I definitely know some would want the hospital because theres a lot of people who get wrecked by deathclaws.