3)Getting rid of points and making it untrained/trained/focused. Lots of people hate this but I can take or leave it. I find points unnecessary, I think people who want "granularity" have a different idea of what a character sheet means than I do, but I don't think the slight ease of use you get from this system is really enough to care about. I have seen some people vaguely annoyed they don't get to mess around with skill points every level, even if it is just adding +1 to int+2 skills they enjoy the illusion of choice.
FWIW, as someone who's completely in favor of the SWSE/4e-style skill system, I always thought the 3.x/standard d20 style skill system was something of a mismatch to the rest of the game. You've got this extremely fine-grained skill system bolted on to characters that are largely built on binary (on/off) choices of feats, class abilities and spells. I think it works a lot better in a pure point-based game like Mutants and Masterminds than it does in D&D.
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