Actually, we just finished some small changes to transmuters, and are moving (very carefully, given other problems) through the process of testing them out. It should diversify the class a bit, further differentiate their art from shapeshifters, and give them a specific kind of (weak, but useful) utility that other classes don't currently have.

Regarding your suggestions:
1) Dex really doesn't matter as much to a mage. You aren't dodging, or doing a lot of finesse-type physical maneuvers like a warrior or assassin might. It effects your inventory size, which can be nice, but it isn't a priority. I wouldn't sweat the dex penalties much. If a situation calls for it, you have Metabolic Quickening.
2) Duo Dimension and Neurological Disruption are very, very good spells. Making them better (given the very recent improvements to ND) than they are currently scares me.
3) Mastery bonuses: These are generally controversial. Some players like that their character will continue to improve over time in that way. Other people complain that they don't like to have to practice to be at their optimum. There's a few things in your post I'd be willing to try out, but my general feeling is that "If you master this spell, all its tactically interesting drawbacks go away" is a bad decision.

valguarnera@carrionfields.com