In addition to the points already mentioned I think the research cost for the more advanced technologies should be massively increased.
I usually play at least large maps but with game and research rate set to the slowest possible pace. At the start, with only a few planets, the research rate is indeed slow and research duration of 10 and more weeks is the norm. That is ok with me. However, in mid to late game when the empire gets bigger and the research capacity is increased, you start to blow through the tech tree like crazy. Even the techs at the end of tree can be research in 2 or 3 weeks.
The consequence is that for example in the missile weapon branch, it is a big deal to get up to harpoons and missile ships with harpoons are the norm for a long time. Once I get to research the next tiers, it isn't worth to design ships with the photonic warheads etc. because I will be able to reach the end of the branch and get nightmare torpedoes so quickly.
Even the acension techs can be researched in only a few weeks - and they are supposed to be those almost magical steps in scientific advance.
Now I don't want techs that take a hundred turns to research, but the current state is to crazy.