All of my modding through Rise of Empires, until Glory and Greatness, was an experiment on my own assets, not custom assets or mod assets. This was very bad technique, because you don't know what changes you've made all the time and what files are necessary or not. Unless you are carefully tracking each change you've altered your core game irrevocably, and you'll have to uninstall and reinstall your files (which I did several times until I got smarter).
Also Through the Ages, I think, is just an earlier version of Rise of Empires, Rise of Empires 3.5 is the top evolution of an VERY early mod called the World is Yours, which became Through the Ages!, which led to Rise of Empires. This means that scattered throughout all of Rise of Empires are several pieces of Through the Ages. They may have different names, better (in my opinion) artwork, no longer actually implement in game, or have just been adopted. But it's all in there somewhere. However, it's a mess!
So I'm not sure what features exist in Through the Ages that are missing in Rise of Empires, per se, so I don't know who how merging them would help. Further, each uses different custom DLL and so I'd need to talk to Asaf again (and frankly I'm waiting spring a bigger project on him for later).
In short, merging them would be very difficult and possibly not beneficial. BUT there may be a way to help you get what you want, nonetheless.
So here's what I propose, after that long-winded introduction:
I will post a fix for Brennus here tomorrow night so his armor isn't pink. Second, If you will tell me what exactly you feel Rise of Empires is missing that was better implemented in Through the Ages I see about fixing it so that Rise of Empires reflects that idea. I need to do a re-release of Rise of Empires, probably in March, that cleans it up and bug-shoots things. So just tell me what Rise of Empires lacks that you feel Through the Ages did well, and I work on that.
I've written a long post because I'm sorry I've been out of touch on this, and feel like you deserve a thought-out answer. I appreciate your enthusiasm on this and would like to get it going. It's just Glory and Greatness has been a substantial project and has eating all of my modding time, so I've been out of it for a while.