I don't think Master Plan can be freely switched to a Tactics check. Intelligence costs 2 points per +1; Tactics costs 1 point per +4. The ability to hit the DCs for the feat becomes fairly trivial if it's a skill check instead of an attribute check.
Quickness takes a -2 for only 1 task, not -3.
Insight has 2 ranks of Defensive Roll, so Toughness should be +10 flatfooted, not +12. Not to mention that I'm somehow missing a few points of toughness: +4 armor +2 Con +2 defensive roll = +8. I didn't check all the math, but this stuck out.
Since the Drain is a perception power, it's maximum DC =10 +PL. It'd already be at that DC without the switch to a skill check based DC. And allowing skill checks for DCs to break normal PL caps on saves means that a PL 10 character could be throwing around DC 40 attacks (+15 skill ranks, +15 stat mod). Also, the normal state of the DC is already mostly equivalent to Clover's Bluff - without the enhanced CHA in the array, her bluff falls to +11. The feats based on weird skill uses generally offer the choice of Sense Motive OR Will (or something else) anyway, so having the power use Will isn't too out of line.
Not to mention that given the importance of Sense Motive in defeating Feints and other skill based attack modes, it's already basically a 5th save. Further mechanics to increase the skill's importance seem somewhat out of line.
Equipment can be nuked by the GM for free, so I'm not sure I'd want to use it for a decent chunk of my combat traits, but that's your call.
While attack and defense fall under skills in terms of trait types, attack bonus can also come from feats (attack focus) and powers (power feat: Accurate). I don't know how the Drain and extra sources of attack interact. It seems weird to leave an attack modified by feats or power feats unaffected, especially since buying attack in that manner comes with a considerable cost savings. Maybe the attack bonus is drained to negatives and then the feats and powers come in on top. That method should cripple attack bonus equally regardless of how it's bought.
IIRC, UP isn't in general use for this game (people are actually using Aura, after all), which may result in the some of the discrepancies above (and more besides). For instance, I think toughness could be bought as a normal save under UP rules - there's no cost difference anyway. Perhaps the biggest difference is that normally Drain isn't staged.