All I would say is that one of the key things points, that you raise yourself when introducing GEM, is the relatively unaltered gameplay of the GEM mod. GEM has become so successful and popular due to the map and scenarios, not any altered gameplay.
In your understandable drive to improve this fantastic mod, I guess there is a danger that you may drop the concepts that have guided the success in the first place. I'm not saying that inclusion of these mods is wrong, in fact for me they look quite exciting, just that in my humble opinion you should be aware of this potential issue.
I guess what you might want to ask yourself is: Would most people chose to play civ, or GEM, with Dale's mod if they knew about it and it was already inbuilt?
There will no doubt be some people, such as me, who enjoy the inclusion of other mods but are unable to put them together themselves, and others, (such as Ace) for whom their playing of GEM is driven to an extent by the fact that the gameplay is unaltered (assuming that any mods they like they can add in themselves).