Yeah I actually read through their forums to see how they were doing it since it seemed like the premier open source RTS since Glest isn't really developed anymore. I am going to do something similar, though I would like to try and do some things better.
How much do you know about what they did? I was thinking of just restarting from their code base because they spent a lot more work on it and it seems more powerful. They have superior modeling, they have a wall system in place, and a lot of other stuff. Although I like to deal with the abstract math of graphics and pathfinding and such I really only like the programming of game logic.
Just from talking to some of the devs about modding capabilities on IRC, it sounds like 0 A.D.'s engine is indeed much more powerful, and a ton of things can be done through javascript without having to actually touch the engine. I've even been toying with the idea of porting my borderline-vaporware Solunar mod from GAE to Pyrogenesis because of that and the more active development, which is what got me talking to the devs in the first place.
They don't have walkable walls, but their wall system does work pretty well in the SVN version (barring one or two little things that I'm sure they're in the process of working out), and even has working gates (finally!). You can't have units on top of the walls, but you can garrison them inside the tower junctions, which is something at least. As far as pathfinding goes, my understanding is that Glest is on a Cartesian (x,y,z) grid while Pyrogenesis uses polar coordinates, which is why their buildings can be rotated arbitrarily. In Glest/GAE, wouldn't walls only be able to be bent at right angles?
On top of that, their AI is much more configurable and different AIs can be assigned to different sides in a match, whereas Glest/GAE's seems to be pretty intrinsic to the engine.