Its been well established that the late games buildings are neither complete or balanced yet. Since more people play the early eras we have that part of the mod much more polished and balanced. Eventually he Modern, Trans-Human and Galactic eras will be balanced too. But until then we have some weird stuff happening where things don't balance or obsolete right yet so late into the game.
Yeah, it is unfortunate that the last era games are almost unplayable at times, after all those hours you spent getting to that point, you pretty much have to restart and just play the beginning eras ; ;