There is not as much choice in regards to factions and morality in Skyrim. The big choices are Stormcloaks vs Imperials and Dawnguard vs. Volkihar.
While the controversy between the Imperials and the Stormcloaks is very interesting, their quests are too similar and their questlines don't affect Skyrim as much as I would like. The Dawnguard vs Volkihar seems to have been better implemented as far as quests go, these factions still have some similar quests in their main quests but all of their sidequests are different.
As for the rest of the factions there is really not much choice. If you join the thieves guild there are no consequences whatsoever and if you do not join them you are missing out on quests and rewards, but no purely good aligned character would realistically want to join them. You can't even try to go against this guild or anything like that. Joining the mage's college of winterhold gives you more content questwise and some rewards, including dragon shouts, so why wouldn't you join? Is there anything stopping you? You will still benefit even if you are no mage.
Stuff like this causes problems in my opinion because I want coices that matter to my character, choices that will shape his/her personality and show how moral or amoral he/she really is. If I can join every guild without consequences why shouldn't I join them and reap the rewards and the extra content? I am only reducing my play time if I choose that I am no mage and I don't want to join the college of Winterhold.
So I came to the conclusion that the next TES game should have a huge variety of different factions. Now these factions will have many different functions and objectives, but what they all share in common is that they have a particular diety that they revere above the other dieties. You will only be able to join 9 of these factions and follow their diety's ideals, this will shape your character to a character with a personality, since he will follow the chosen deities for his own reasons. Of course these factions will all have unique rewards including Daedric and Aedric artifacts in the end of their questlines. These gods will includ the Daedric Lords the 9 Divines and other gods such as Sithis.
Joining these factions will also have consequences. If you join a secret cult devoted to Talos the Thalmor will try to hunt you down. If you join the vigilants of Stendarr you won't be able to worship any of the Daedric lords. If you join any of the Daedric lord you will be hunted by the vigilants of Stendarr. These consequences are just examples and there are many more that could be implemented.
There are many factions that we could have with this system.
For example we could have:
- The Vigilants of Stendarr who are devoted to Stendarr and hunt down all the Daedra and all of the Daedric followers.
- The Thieves Guild who worship Nocturnal.
- The Dark Brotherhood, assassins that praise Sithis.
- The cult of Dibella, skimpy Priests and Priestesses that practice the "Dibellan arts", if you know what I mean.
- A vampire clan that worships Molag Bal.
- A pack of werewolves, devoted of Hircine.
- A college of mages that praises Julianos.
- A secret society that worships Talos away from the eyes of the Thalmor.