I've been giving some thought to the design of PCs, since I'm going to be the GM and all, and I'm finding that while I can just about stat them out in HERO while sleeping, I'm having a little problem getting the kind of subtlety that I want out of M&M.
Odd, I have the exact opposite reaction. I suppose it's a matter of what you're used to.
One of the nice things about villains specifically, and NPCs in general, is that you don't need to worry about their point costs. Set the PL, assign them whatever fits, and you're done.
As a courtesy, I'll throw together a build of Dr. Zues. Begun at 02:15 local time.
PL 9 [Allowing him to really tear into a bunch of PL 6 characters while still being beatable, if only barely]
ABILITIES:
STR 27 (+8)
DEX 15 (+2)
CON 20 (+5)
INT 24/2 (+7)
WIS 18 (+4)
CHA 17 (+3)
SAVES:
TOUGH +10 (+8 without coat)
FORT +9
REF +6 (+12 vs visual Dazzles)
WILL +8
SKILLS:
Acrobatics 5 (+7), Climb 13 (+18), Craft (electronic) 8 (+15), Craft (mechanical) 8 (+15), Intimidate 6 (+9), Knowledge (physical sciences) 8 (+15), Knowledge (technology) 8 (+15), Notice 8 (+12), Sense Motive 8 (+12)
FEATS:
Acrobatic Bluff, Attack Focus 3 (melee), Equipment 5 (various bases and vehicles), Improved Pin, Inventor, Master Plan, Power Attack
POWERS:
Device 4 (Lightning Gun, easy-to-lose, Restricted: Size Large or larger),
Device 4 (Tesla Bombs, easy-to-lose),
Device 1 (Protective Costume, hard-to-lose),
Enhanced Intelligence 22,
Growth 4 (permanent, innate),
Protection 3 (thick hide),
Super-Movement 1 (swinging),
Super-Senses 2 (low-light vision, scent)
Lightning Gun: Blast 9 (Area: Cone, Range: Touch;
Alternate: Dazzle [visual] 9, cone area;
Alternate: Blast 3 and
Dazzle [vision and hearing] 4, cone area)
Tesla Bombs: Blast 6 (Area: Burst;
Alternate: Dazzle [visual and hearing] 4, burst area;
Alternate: Stun 4, ranged, burst area)
Protective Costume: Protection 2,
Sensory Shield 3
COMBAT:
Attack +5, +8 (melee); Damage +8 (unarmed), by device; Grapple +21; Defense +8, +4 flat-footed; Knockback -6, -4 without costume.
DRAWBACKS:
Noticeable - Protection power, due to thick hide.
Noticeable - Enhanced Intelligence, brain in a jar.
Vulnerable - +50% to flattery; sense of superiority.
COMPLICATIONS:*
Hatred: human race in general.
Obsession: gain power to be free from human influence.
Obsession: "punish" humanity for it's monstrous actions.
Prejudice: freakish experimental ape, shunned by man and ape alike.
*As an NPC, Dr. Zeus doesn't get Hero Points for his complications. These are included as role-playing notes.
He can do everything you've requested. Feel free to use him, ignore him, or rebuild him. Good luck.
Finished at 02:31 local time.
Edit: I realize this doesn't answer all of your questions, but I'm wondering if it clears up the underlying concepts. If it doesn't, I'll try helping out with some of the specific issues you've raised.