Pathfinder is definitely a lot kinder to under water battles when you don't have some way to breathe instantly than 3.5 is.
Still... I think water is a cool avenue for adventurers.
3.5 is already pretty generous. Actually, looks like the rules for drowning are identical:
http://www.d20pfsrd.com/gamemastering/environment/environmental-rules#TOC-Drowninghttp://www.d20srd.org/srd/environment.htm#drowningBasically you can fight for a number of rounds equal to your constitution *score* (not mod). Then you start making a fort save that grows from 10. If you take only 1 move action, you use half the air that round.
(I'm only sharing this because it's kinda funny. Even untrained, adventurers are *amazing* at holding their breath and remaining calm underwater)
As for swimming in heavy armor... Technically it's just a penalty to the swim check from what I can find. But it's *double* the normal armor check and encumbrance penalty. You're trying to hit 10 to move in calm water, 30 if you want to move at normal speed instead of quarter. 6-9 you don't move, 5 or less you fall underwater.
So in full plate with a heavy shield and a medium load, you're looking at (6+2)*2+(3*2)=18 penalty. DC 24 to tread water, DC 28 to move.
Pretty tough! Keeping a light load helps a lot though, as would stowing the shield (stowing the armor would help a lot more, of course). With about a dozen ranks a warrior could probably swim across a lake in the full kit. They might hit the bottom first though, but they have plenty of air.
But yeah, if they have waterbreathing then they're better off trudging along the bottom. I'm not sure what the rule is for that but I assume it's half-speed, or maybe full (though that would be silly).