Like in Morrowind, (EDIT: most) guilds/factions in Skyrim should have at least one "enemy" faction, and you should only be able to join one (or at least have to make a choice at some point). Like in Morrowind, they should have some "opposite" missions; i.e. the same mission but taking the opposite side depending on what faction you belong to (think Figters/Thieves or the House missions in Morrowind)
They should especially have something like the Houses in Morrowind, which with the civil war in Skyrim should be easy to implement several competing political groups.
With guilds, (EDIT: most) should have an opposite/enemy. To use Obivion as an example, the Necromancers should have been a joinable faction with their own missions against the Mages Guilds, or the Blackwood Company against the Fighters Guild.
One reason I really like this kind of setup is that it adds great replayability to the game - having good and an evil character that will not have to go through any of the (exact) same quests, which gets boring and greatly deters starting a new character just to play through the same several hours of basic quests just to get to the new content you want to experience.
Examples:
Necromancers vs. Mages Guild
Thieves Guild vs. Dark Brotherhood
Fighters Guild vs. [something like Blackwood Company]
"Houses" like Morrowind, but lore-appropriate counterparts for Nords
Imperial Legion should return as a faction, perhaps as an alternative to the Nords wanting to leave the Empire (Legion works to keep Skyrim in it)
***Disclaimer: Yes, I know that Bethesda has already completed the game's content by this stage in development but I like putting my opinion out there nonetheless.
Sadly, what you are suggesting is the pathetic and weak 1v1 crap I have been saying has been nothing but a giant..ugh...annoyance! Not to mention, joining goody goodies or puppy kickers is not a choice, it's [censored] stupid! There is no dimension when I'm joining a bunch of puppy kickers, as they're all pretty much end up the same, just killing a person a different way, and save deal with being with goody goodies.
Again, more "we like this group, hate that group, and this group is meh" and less "Necros vs. MG." Guilds and organizations should mingle, take jobs from each other, handle jobs from each other, and so on! More dynamic!
If this is the impression I gave, I apologize. I was not suggesting such a rigid structure and my examples were only examples, presented without the necessary plot/reason behind them; and I do not advocate making every faction pure good or pure evil, but I believe TES presents factions for the most part as either good, neutral or bad. In short, I agree with everything you said, except the insults. I did get "the point with Morrowind", and I am advocating a return to Morrowind-like factions, as opposed to Oblivion-like simpleton dullville factions where you simply do the quests and become leader of every faction, so implausible and dull.