The focus energy one (recently reported) has already been proposed as an Anti-Mewtwo thing (all eeveelutions can get it by hanging around as an eevee for a bit longer on yellow). Flareon could smack up Mewtwo with Fire Blast or Take Down, Vaporeon could use Surf or Hydro Pump, and Jolteon was already mentioned (I forget by who, but its a damn good idea).
Also, using moves with recoil apparently doesn't effect you if you knock out the other guy, nor does it if you break a sub (maybe just if you hit the sub). This would make a nice combo with Focus Energy, I think...
The other big one you missed is the power down of ALL sleep effects. Now the maximum range for the sleep counter is three (used to be seven). While getting rid of the high numbers seems OK, I really have an issue that the following rules are in effect:
1) One asleep at a time
2) Sleep from 1-3 rounds
3) Even distribution so 1/3 of the time you wasted an attack, versus 1/7 previously.
If 1 didn't come up so much, I wouldn't bitch, but.... well, I already posted on this.
The side effect chances are generally documented, and various moves now feature more or less frequent things. This is good, in my opinion, though I think Thunder should paralyze 30% (come on, it MISSES 30%!). Most of the changes are decent, but I'm sad paralyzation isn't as good anymore.
Blizzard has a lesser chance of freezing. Good call. I think Blizzard is too strong. It's like Hydro Pump and Fire Blast, but can kill in one hit, and is more accurate. Additionly, Ice is good against everything (virtually). This move shouldn't be 120 strength in the first place, IMO (Ice Beam should be weaker, too). I just don't feel that Ice deserves a place as the elemental big boy over the rest (especially fire). Oh well, too late to bitch...
Why do they favor Mewtwo (almost all do)?
I don't know. It almost looks as if they meant him to be unkillable, and viewed the ways around that as being glitches (Electrode could go first and paralyze him! Make paralyze suck! Once asleep, he is mortal! Make sub block it!).
Someone said it was so we would find Gold/Silver that much more pleasing...