Just thought I'd pop in to say I really support this idea. I really hope you manage this! :twirl:
Well, that mainly would require lots of scripting, at least for the most basic version. Sadly I'm only good at thinking ideas and very basic modding

I love the idea. I always feel like I'm just stalling historical events by avoiding the MQ. What if you didn't use an alternate start mod though? Should you have to drop the amulet somewhere for the champion's quest to start?
I've thought about that and found two possible ways to do it, both require you not to have delivered the Amulet to Jauffre yet:
1) A quest popup that shows up the 1st time you sleep with the mod activated, telling you that the intro dungeon was a "weird dream", and removing the Amulet of Kings from your inventory.
2) (Inspired from another no-MQ mod, don't remember which one now): You give the amulet to Jauffre, and tell him you're not interested on doing anything else for him, then leave.
i could see the "Hero of Kvatch, Champion of Cyrodiil" as someone you never meet, but always seems to be just around the corner and out of sight. For example, you could walk into the market district and someone would run up to you and say "Did you just see that? The Hero of Kvatch...just shook my hand! He was just here! I can't wait to tell my husband!" *runs off*...
A good idea, if the Hero/Champion is not to be implemented "physically".
Great idea. I've actually got my own idea for an, er, variation of the main quest, and I can actually see both ideas working well together.
My idea is basically, what would happen if you LOST the battle for Cyrodiil? I imagine that all possible gates open, the sky turns permanently red, and Daedra and teams of Dremora swarm the cities, destroying everything in their path. We've got Enhanced Daedric Invasion right now, which can simulate some of the city invasion stuff, but I'm looking to make Total Daedric Invasion, you know?
Anyway, my idea for triggering this was to insert some quest near the end of the main quest that lets you choose between saving the world like normal, or letting everything go to hell. But if you're not the hero, and presumably the hero's out there trying to save the world, there could be a whole quest line where you track down the hero and TAKE HIM OUT! Destroy him (or her), I mean. Basically giving people the option to play a truly evil character, which would certainly be fun.
I like it

Maybe even with all the cities "Kvatchelized" and a post-apocaliptical survival questline. Would require a lot of work, though, at least that idea (mine could be done entirely with scripting, if I'm correct).