Well I do agree that certain terrain types should be more valuable. Specifically, I think that freshwater grassland and floodplains should be very valuable because that (for me) makes sense in terms of what you'd look for when settling a city. In contrast, mountains and jungles should be bad tiles because you can't really get much of anything from mountains, and jungles are notoriously hard to travel through and live in.
I don't mind a minor science adjacency bonus from mountains and jungles, that both makes sense and adds flavor to these tiles (as a compensation for their otherwise poor nature). However, I do object to the fact that mountain adjacency bonus seems to be the major source of early science, which is both nonsense and bad for gameplay (because we know how important early science is for the snowball effect on the game in general). Also, the fact that jungle tiles not only give science adjacency bonus but also have godly yields themselves even when unimproved is just plain absurd.
Agreed. I think the science yields from mountains and jungles are too high. I think historically, bonuses from mountains came fairly recently with observatories being placed on mountains and jungles being studied for medicine. To have significant bonuses early in the game is a bit silly, IMHO.