Well you're doing it right anyway if you avoid the puzzle rooms, because those are the only two that don't have one of the strongest equips for each character. I never even see those rooms on my playthroughs, 'cause I always bail out by failing on purpose to make sure I get the weapons.
The ball solitaire is indeed difficult from what I remember, but that one never did bother me as much as the logic puzzle. Agreed on the isometric view as well--it's surprising the action rooms are still as fun as they are despite it.
On a separate note, I never got why the quiz guy was called Dr. Topper. Goes right along with other naming weirdness in SMRPG, like Neosquid. I mean, what in the world was Ted Woolsey thinking with these names??
It's the kind of unsolved mystery that bothers me when I think about it too much...