Huh, I didn't realize multiple sources of damage bonus were multiplied, not added. That does make a big difference.
I just feel like if water damage compared with fire damage AND has several healing/buff skills, that makes pyro seem lackluster. Pyro after all seems to be the go-to damage tree. A water mage might have some damage skills at their disposal, but that's never going to be their main niche. Maybe some other source (like a talent) could improve water damage, maybe sacrificing healing, if you really want to go for a water/ice damage build.
However, I have to agree that it feels lame that MANY skills are entirely unaffected by leveling up the ability tree and/or the attribute. The issue is its hard to subtly improve certain skills over time. How do you buff, say, Haste? I suppose you could increase the movement speed it granted. What about Walk in Shadows? Pretty much either reduce its cooldown or increase duration, but that has to be over several points rather than per point of ability or attribute, and the benefits can greatly swing its power. A 4 turn CD to 3 turn CD is significant.
So I dunno. Probably simply not possible to make every skill affected by improvement, or it would take a lot of individual tweaking (and coding) of each skill to improve them over time. But it does seem like attributes and abilities are overly narrow in their benefits. I hope they find some better middle ground between universal benefits and simplicity and balance.