Hopefully the process will also aid those who plan TC's that don't want Skyrim stuff getting in the way too, but MQ101 is hardcoded as a launch point so it has to be dealt with.
Duplicate MQ101 and give it an ID of MQ101A
Edit MQ101A removing the character generation part.
Edit MQ101 so that it ONLY includes the character generation aspect. Have it take place in some generalized area, such as an interior room. When it is done, have a forced dialogue that has two options. Play Dragonborn storyline and Play [insert title here]
Choosing Dragonborn will end MQ101 and begin MQ101A
And since everything about the main quest is now in MQ101A, it should start the game normally. The most notable change will be that there would be no perspective change for creating the character and the story events would progress...
The tricky part will be that EVERY single reference to MQ101 will need to be updated to refer to MQ101A. Otherwise the quest will be broken horribly.
A mod that does at least this should be released as a .ESM so that is serves as a clean slate for those wishing to produce alternative storylines. The option at new game start should always allow the player the option of playing the normal main storyline as well as the alternative.
It should be noted that everything I just said is based on my admittedly limited understanding of how the start of the game works. If I am wrong about any of it, please correct me.