Yeah, there are some serious issues with cost/benefit on some stuff. Without leveled flats, they're really not worth much to start with, and you need a huge amount of production to make the upgrades valuable in the short term. They eventually pay themselves off, but 2.5% takes a while when you could have done Aid Research for the same cost, and not spent a resource on top of it. That your planets are probably going to be really good at producing buildings compared to how well they can produce research just makes it all the worse. You can do a cluster around a Space Elevator, more than double your production, and make those poor science buildings take twice as long to pay off.
Your ability to make a planet "better" at science in a similar fashion is somewhat severely restricted. These Space Elevator clusters are also smart to build on every planet, because they greatly expand the ship production capability of the planet, are downright necessary to actually build those science structures without taking hundreds of turns, and end up farming more science or money in the end anyway. More ship production also being a method of gaining research and money yet again compounds the issue...
The plus side is that planets don't go from taking 20 turns to produce a 1 attack ship, to single turn producing a 6000 attack ship. I wish that were a flagrant exaggeration. The scale up is unmanageably exploitable in vanilla GC3, what we've got is a far superior progression, it's just got some major issues at present. Hopefully soon to be fixed issues...