1) AP reduction
there would have to be a limit to how low cost can go, because there are characters with already low cost AP skills and further reduction would make them overpowered (like already mentioned Ragnarok), e.g. cost of skill cannot go below 2AP
for me reduction by 3 seems bit too much as it reduces cost by one move essentially. I would prefer to see reduction of 2 colours by 2 (preferably with new combinations, not the usual Y/R, B/P, G/B) and of all colours by 1
2) HP Regen
Definitely %, because it will scale nicely with your characters.
It would hard to make set amount that wouldn't be overpowered at low levels and not meaningless at high levels at the same time
3) Countdown reduction
as in 1), a limit to how low countdown can go. I would say one or two turns.