Number of strings
Type or bridge
Switches and knobs and other cool stuff
Go go go!
I would do:
Headstock - reverse headstock (never played one but I heard they're metal)
Neck shape - thin and flat, like original Wizard or Parker Fly thin
Neck wood - I don't know enough about neck wood materials to choose
Body shape - A thinner Ibanez RG. While I like Parker Flys, I never got into Ibanez S series. But since this is my ideal guitar in make believe land, a thinner RG that is slightly rounded along the edges.
Body wood - Some of the best sounding guitars I've played have been Alder.
Strings - 6
Bridge - Some sort of floating trem that stays in tune, with Piezos a la Parker.
Pickups - HSH, although I don't know enough about pickups to make a choice here
Knobs/switches - volume, tone, a Piezo toggle switch, and I saw Chris Broderick of Megadeth had a kill switch on his guitar and I thought that was kind of cool so one of those, too.
Headstock - Tom Anderson shape
Neck shape - Something like an RG550 or an S series
Neck wood - Maple/Maple or Maple/Ebony
Body shape - Probably the John Petrucci shape. Kind of like a thicker S series shape. I also love Tom Anderson's S shape
Body wood - Alder or Swamp Ash most likely, and possibly a maple cap
Number of strings - 6
Type of bridge - I'd have to test them all. I like the newer Kahlers and the Ibanez ZR bridges though.
Pickups - Single coil in the neck position, humbucker in the bridge, and nothing in the middle. Probably Air Norton and Norton in the neck and bridge.
Switches and knobs and other cool stuff - TWO FUCKING WAY BLADE SWITCH. GREAT FUCK WHY CAN'T I FIND THESE? And a volume knob.