I won't claim to have played all of the MQ mods, but two specifically jump out at me as being quality work in one way or another: Darknut's Greater Dwemer Ruins, and Great House Dagoth. Unfortunately, these are not compatible with each other, and honestly Great House Dagoth has a lot of issues and limitations that it really shouldn't and/or could have been avoided. At any rate, these mods make the main quest experience much more full and "epic". This is the sort of thing Main Quest Enhanced would seek to do, filling in the gaps where lore suggests the possibility of such, but which are impossible in the vanilla game. What follows is an outline of what MQE would add to the game. You are free to incorporate any of these ideas into your own mods. While I would certainly like to, I can't say for sure whether I would ever end up developing these ideas myself.
1. On the divinity of the Man-Gods
a. Vivec and Almalexia
TES3 starts us off in a Morrowind where the the local man-gods known as the "Tribunal" are waning in power. They have been away from Lorkhan's heart for too long, and have lost two of the three tools needed to extract the power from the heart in ill-fated attempts to make it up the mountain. Yes, the Tribunal are weakend: Vivec alone powers the Ghostfence, a task that is becoming increasingly difficult for him.
While the Tribunal are weekend, I think it stands to reason that while the Heart of Lorkhan still beats, they are still divine enough to resist death. In the vanilla game, the player may kill Vivec at any point with any weapon he feels like just about. This never sat well with me. While the Heart is still intact (during the MQ), I believe Vivec and Almalexia should be unkillable except through the use of Trueflame. It seems as though in order to slay anything even close to a god, a special tool ought to be required. In the same vain, Vivec and Almalexia should have noticeable stat reductions after the Heart of Lorkhan is destroyed. If I recall correctly, in the vanilla game your inevitable battle with Almalexia is no easier even after her ties to the heart are severed completely.
b. Living Sotha Sil
How many people were disappointed to find Sotha Sil murdered towards the end of Tribunal? I certainly was. Sotha Sil should be a living character in-game at least up to a point, and the option to save him through a sub-quest line should have ALWAYS been available, truly one of the biggest letdowns in Trib. Just like the other two gods, he would have higher stats pre-MQ completion and lower stats post-MQ and while the Heart still beats, Trueflame would be required to kill him should the player decide to do so for whatever reason.
c. Defeating Dagoth Ur
Like the other heart divines, Dagoth Ur should be defeatable with Trueflame. The ramifications on the main quest would be the hardest part of this to implement: a lot of things would need to change post-MQ, which I will discuss in the next section
2. Alternative Endings
a. Return of the Tribunal
If the player defeats Dagoth Ur without destroying the Heart of Lorkhan (through the use of the god slaying Trueflame), he should have the option of allowing the Tribunal to rejuvenate themselves with the power of the Heart, which they had attempted to do countless times before the advent of the Nerevarine. In this case, Red Mountains post-MQ state would be the same.
b. Great House Dagoth
The player should be able to answer Dagoth Gares' invitation to join Great House Dagoth. Like in the mod Great House Dagoth, the 6th House would be treated as a joinable faction. The player character would be able to follow a full transformation from Corpus Stalker to Ash Vampire through Ur's guidance and council. If I were to develop these ideas myself, I would certainly attempt to contact the author of GHD and attempt to salvage the mod into something more usable for this project.
c. Lord Nerevarine, Heart Divine
The player should have always had the option of succumbing to the allure of becoming a heart-divine himself, with the option of becoming the highest Man-god worshiped by Morrowind's Temple. To fully flesh out and explore this option, the player should be given the option of having a city built for him (named Nerevar or Nerevarine, like the cities Vivec and Almalexia are named after their patrons), or the option of withdrawing into a dominion of their own devising (like Sotha Sil's Clockwork City) or possibly both. This option need not conflict with a or b: allowing the Tribunal to rejuvenate themselves would still be an option but not required; should the player join the 6th House or side with dagoth ur in the end rather than destroy him, the option for a city would be replaced with the option for a Citadel in Red Mountain, and the option for Temple faction tie-in would be replaced with an option of slaying the Tribunal, disabling Ghostfence, and spreading the blight across all of Vvardenfell.
3. Area Overhalls
a. Red Mountain
Red Mountain is the tallest mountain in all of Tamriel, but if I recall correctly, it is not even half the height that Morrowind can handle in it's engine. The entire region needs an overhall to bring it more into lore, the mountain needs to be much much taller. I also like Darknut's idea to put a tower on Dagoth Ur's citadel at Red Mountain's peek which to me is reminiscent of the Adamentine Tower, a very nice touch considering the Dwemer often sought to emulate the et'Ada.
b. Sotha Sil
The Clockwork City is but a small piece of Sotha Sil's domain as has always been hinted at. If the player should decide to do quests for the wizard-divine, it stands to reason that he should be allowed to explore the greater depths of Sotha Sil. "Sotha Sil" would be a massive interior in the style of the Clockwork City, populated with the various fabricants created by the least-known heart divine many of which I should think would be sapient.
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And that's just about it, at least that is all I could remember from the things that keep popping into my head every so often. I'd very much like some feedback on this at the very least. Best case, I eventually feel ready to pick these ideas up and make something of them myself, but I hope for now it is an interesting read or perhaps an inspiring one.
I would especially like to know if I am terribly wrong about anything that would totally break one of the ideas presented.