My suggestion for the main quest:
No more invasion scenarios. Invasion has been thoroughly overdone by Oblivion.
Main Quest: Invasion by Mehrunes Dagon.
Knights of the Nine: Invasion by Ayleid Meridia-worshipper who's mad at the Nine and pissed off about Sword-Theory.
Shivering Isles: Invasion of Sheogorath by
.
I'd much prefer a Skyrim politics-based MQ akin to Daggerfall, where you are the pawn of pretty much every major power in the region. I won't speculate on what the objective of the MQ might be, as that's an impossible task, but here's how I'd like to see the MQ behave. Most of it relates not to MQ substance, but to MQ structure and style.
1. Subtle start:
A MQ that just screams at you, "Go start on this path now or all hope is lost!" is a good way to svck the player into a linear game. It's also potentially good for things that have linear plots, such as books or movies. However, for a game that prides itself at being completely sandbox and non-linear, a MQ that pushes its own importance upon you from the get-go is bad design. It guilt-trips the player into starting almost immediately, because the beginning was so grand and epic. It severely guilt-trips the character into starting immediately, because there are few viable and non-baggage-carrying ways to roleplay that character to where (s)he doesn't care and won't immediately act. Therefore, the MQ opening must employ subtlety. A delivered letter, or a hint of information. Something that holds intrigue and can catch player attention, but something they can still stuff away and say, "I'll get to that later."
2. No Letters of Recommendation:
You start out as a nobody. You are not ordained by the gods. You are not given the golden seal of approval by a dead ruler. You are an unknown quantity to the world, and therefore you are insignificant. Even to vital quest-givers.
Especially to vital quest-givers. To get anywhere with the storyline, you have to first get some recognition, and secondly, you must then grease the wheels (moreso than Joke! Admire! Coerce! Boast!, anyway). And recognition does not come solely from doing random good deeds across the land. That's all well and good, but political recognition is what matters most. Yet earning some trust (or even acknowledgment) from political rulers is a long and tedious task, comprised of playing the right angles, doing the right favors, and maintaining face all the way up the proverbial chain of command. In other words, significant semi-"freeform" work would be a requirement before getting into the real meat of the story. Which is good, because the meat of the story should always be saved until the intermediate plot.
3. Ability to feasibly walk away / Main Quest Intermissions:
Going hand-in-hand with a main questline start that foists its own importance upon you at the beginning is the main questline that never allows you room to breathe. Hence the need for times and places to come up for air. You just finished a job for one of your employers? They might congratulate you, compensate you, and then inform you they'll need a week or two to see how things pan out before they proceed. Instant break on that avenue of the MQ. Sure, since this would be a Daggerfall-esque political story, you could try your luck working for one of the other rulers while you wait, but that decision is not forced onto you by the game via "this is the next step, so go do it." And when that time-period passes, when the employer sends word to the player via letter/messenger that they have another task at the ready, the player has now been away from the MQ long enough to actually have the unbiased choice of continuing, or perhaps putting it off for a bit more so they might finish some unrelated work.
4. The Endgame pulls all the stops:
Chances to take a breather significantly reduce as the player passes the middle-story and enters into the beginning of the end. This is where all the epic, all the guilt-tripping, all the sense of "you really need to do this now" and urgency comes in. This is where the heat is turned up. And as it's coming in at the endgame, it's not falsely or arbitrarily imposed. The questline no longer has to push its own importance on the player. Since the player has now had the whole previous quests to discover and learn things over time, the player will push the importance on the questline, aided and abetted by endgame events and dialogue (And of course, the endgame does not literally mean "the end." For example, meeting with Vivec and starting the hunt for Kagrenac's tools was the endgame, even though the fight with Dagoth Ur was the end).
5. The End is not really The End:
While it might work in linear stories, no plot of the magnitude TES tries to convey climixes and ends in such a clean manner. "Killed Dagoth Ur? Well, the land's saved, so I guess we're good!" "Stopped Dagon? Great, now we've got nothing left to worry about!" Sure, you can still keep playing, but the MQ is done, and any actions you undertake to attempt to RP furthering it are RP and nothing more. No MQ should just end with the climix. Whether it's ironing out recovery details, or mopping up the leftover mess from the antagonist(s), or untangling bureaucracy, SOMETHING has to be there to let you gently down off of your proverbial MQ-high. After all, every story needs some form of epilogue, no?