I think they are at least partially compatible, but how much so? Can generation 1 and generation 2 cylinders easily and effectively be combined in one pneumatic pipe system? I.e. a set of pipes, tubes and other parts that exchange the air and are pressurized by the same pump. And how can possible problems be overcome?
https://www.wikiwand.com/en/Lego_pneumatics describes the various generations.
They describe V2 more as generation 2.1, pistons changed, but tubing and t-pieces stayed identical. Therefore I think it's safe to say that it's entirely compatible with all pneumatics from 1985 on ... The pneumatics prior to that is a different story...