First
Skyrim was designed to be an exploration game, but the directed (quest centric) gameplay and the attention given to the main- and faction quests somehow seem to devalue this by a huge deal. Your immediate surroundings no longer matter, and the town quests (aside of daedric ones) pretty much feel like generic bandit slaying and fetching quests with no real value behind them.
Second
Since these faction quests are so extremely good compared to the other quests out there, characters tend to complete them all, becoming the leader of all factions (A Companion Archmage of Winterhold and the leader of Thieves Guild while listening to Sithis). It's all a bit anti RPG and kills replay value and immersion.
So behold: Alignment System
Lawful, Chaotic as the first part, and Good, Neutral, Evil as the second.
Most meaningful actions in the game (such as dialogue options, quest choices and gameplay itself) will contribute points to an aligment in this axis. First part is defining if the player plays chaotically or lawfully, the second part determines if the character played is good, neutral or evil.
At later stages (some arbitrary number of points accumulated), players are invited to a guild/faction depending on what their playstyle up to that point has been. The higher the point accumulation goes in this axis, the more that faction rewards the player with resources and items. All factions ignore the character until it's alignment suits them.
Imperials: Lawful Good
Stormcloaks: Lawful Good
Companions: Chaotic Good
Thieves Guild: Chaotic Neutral
Dark Brotherhood: Chaotic Evil
Mage's Guild: Lawful Neutral
Now, you can only choose to dedicate a part of yourself to only one of these factions. Imperials and Stormcloaks are both in the same category, but rule each other out by default.
Actions that give you points in this or that way would then be tied to everyday tasks such as quest dialogue options, persuation, intimidation, lock picking, stealing, trespassing, killing bandits for bounties, doing "good" quests, giving gold to beggars, etc. And eventually (many many actions later), you would get contacted by a faction member with a note that you're expected to join them in some RPish manner.
This way, the whole game shifts
focus into the mini quests and roaming the wilds gathering some sort of karma, and paces the game better in general and gives the feeling of being that exact character that you play. You will be only one thing per playthrough, and you get to explore the world "sooner" as other options gray out. Characters feel more unique, and replay value should be better.
Also, a system like this, implemented early enough, would provide a solid framework for future quest designers that want to expand a certain branch/faction/playstyle.
So the question is: Is this kind of mod like building the wall of china with domino chips? With my limited modding experience I think it might be possible, but writing the quest dialogue would be a massive job.
Thoughts?