Motion.

Lots of it.

One of the ideas behind Tron: Legacy was to capture elements of Capoeira and Parkour and (despite the fact that I saw far more of the former than the latter) I think I buy that idea.

Vehicles are important.

The Isos walk in from the wilderness and get wiped out to a man, CLU rules the grid with lightgliders and lightcycles and lightfighters.

Some kind of Chase mechanic.

Maybe a riff on Dead Weight's Flow.

There should be ways to escape, race, outpace.

Program hacking and manipulation is a near-mystical ability.  We only really see the (somewhat messianic) Kevin Flynn do that sort of thing.

Weapons are simple shapes, Rods and Discs, so any relative power might well come from the User rather than the form.

Character types should probably account for Isos, Users, Programs (and Program types... Viruses?) it would be nice to resurrect Bit and his ilk, although I doubt they would be playable.

Hm... bit of a stream of consciousness, that, sorry.