After having played around with the new skill system a bit - I noticed that passive hull regeneration, while it can be modified by gear and captain skill, greatly varies between ship classes.
For instance, and Assault Cruiser Refit (T5U) shows a native rate of 146% per minute, while a Jem'Hadar Dreadnought shows 80%, all other things being equal.
Not that it does not make sense, but should this not be a stat that is displayed in the ship vendor?
Remember, STO is nothing but a cosmetics game, where only the rule of cool matters. The game mechanics are intentionally out of balance, don't try to "optimize" anything, as it would just frustrate you.