I think it will be hard to remake the main quest, everyone will probably have played through it by the time they play the mod, so by the time they come to F3C, even if you do a bang up job, they'll know the general structure... not have a feeling of suspense, and while they might appreciate your approvements they won't be fully enthralled.
I sidestep this by completely jumping out of FO3 altogether in my mod, but my idea for F3C would be:
- Pretend the main quest was lifted entirely from the game.
- Put back the locations/quests as subquests that you like, but detach them from the main quest line, just make them fun things to do in that location (like all other quests).
- If there is a location you want to use in your new main quest, leave it blank, for instance Raven Rock you might want to entirely remake if you plan to use the Enclave.
- Create a new main quest entirely, perhaps nothing to do with good old Dad.
The reason I suggest it is that players will have no clue exactly what is going to happen in the game. They'll have a reason to seek out the quest. You'll have creative liberty to make a quest that actually has a cool structure (like the more spread out, red herrings version described at one point in this post). You can still make use of objects of course, like the Enclave, or the GECK, but the more variable it is, the more I think people will ultimately enjoy playing it.
As for main quests, I'll throw out some briefs:
- The Enclave comes back. Maintain and expand the Enclave showing up in force, make another justification, but the point is they are a real threat. Even better, make it a staged invasion, perhaps spreading out from Raven Rock, and you need to stop them before they kill every thing in the Wasteland.
- The GECK quest, your goal in the main quest is to create a new settlement in some barren part of the waste, and for that you need a GECK. Yes, its a rehash to the setup story for Fallout 2, but this time you actually create the settlement, and your goal is to negotiate treaties with various factions, encourage people to set up shop, and protect the growing settlement from some monster force.
- Something entirely new. My personal favorite, something we haven't seen before in a main quest, let your creativity run wild, and plot out something that can be strung through the many locations in the game world.
+ Civil War in the BOS
+ Tyrannical Vault 101 Overseer gets overthrown and explore what happens when they set out from the only truly functional vault in the area.
+ It's DC, get into the Great War and explore what went wrong, somewhere has to have some data.
+ Mad Raider is trying to become Napoleon 2 (well er 3?), help or prevent him from uniting the wastes.
So on and so forth. I personally prefer being surprised, and I can just see myself, you guys putting dozens of hours into it, and I still play through it and go "wow that was nice, but na, I'm not going to detour to Tenpenny Tower because I know Vault 87 is my next major point along the path". Red herrings are very valuable, look at their use in Fallout 1, and that is hard to do after everyone has been hand held through the structure of your main quest, and knows every waypoint.