@Hydromancer: Okay... now I'm utterly baffled on how your actually expecting to do alternate timelines, at all. Try giving us an over view of the basics of how you plan on making this work. Apparently your thinking is completely off kilter from mine... and I'm not sure what specifically your planning on doing... which makes it awful hard to comment on.
From what this thread has shown so far, alternate timelines requires:
1) New *Ages*: These must be defined and the way to activate them turned on.
2) New Techs: Which used for instituting the specific features of the *Ages*. The alternate method involves adding in hundreds of bonus to the dozens of existing techs and having the turn on and off dependant on the 'alternate timelines' tag being clicked.
3) a disablable 'Alternate Timelines' options: That or lots and lots of new game options under a submenu lable 'alternate timelines' in the custom game menu.
The biggest issue is your making Alternate timelines an add on option rather than a separate mod. This is the area that seems to be causing you issues. Personally I think its less work to make C2C: alternate timelines a separate mod from the vanila C2C. If everyone like certain features you can intigrate them into the main version.
All this is mainly ease of interface issues.
---
The only really new things I suggested was making certain techs require a project(s) to be built before they can be researched, no project that *Age* never happened. Thus the techs can't be researched. Which unless something truely odd comes up should be the same thing as adding previously researched tech requirements to a tech. Making projects require a wonder(s)/ tech(s)/ building(s) to is mostly existant. The projects themselves are what count as the trigger flag for the bonus of that *Age*. Again the specifics of the *Age* are a separate issue.
Again this is why I asked if projects had any particular restrictions unquie to them. Making mutually excusive projects that bind you to a particular *Age* of an Era (Ancient, Medevil, Modern) I suggested 3 *Age* paths, at least, per era one of which is the core vanila version. All the *Age* paths end up at the same group/single tech that advance to the next era.
To keep thing move level, once unlocked every tech can be researched by anyone (or at least those that are in diplomatic contact with someone in one of the noncore *Ages* of any particular) once it is unlocked... however with out the project you don't have access to most of the unquie features of that age. You do get cross pollination bonuses for learning/acquiring techs from other *Age* paths. Knowing the tech will give you access to promotions for fighting aginst that type of unit as well.