Mechanical/Electrical
-LED lighting: Yes
-Brammo styled headlights: I'm very satisfied with mine. Once they're properly adjusted, they work great!
-ABS: No
-Ensure the exhaust system will last
-Stronger rear uprights/bearings
-Switch to a 4x100 hub setup to make lots more wheel setups available
-Establish a relationship with Rays Engineering and use the model TE-37 wheel of the correct size/offset for the Atom.
-Brammo style adjustable A-Arms, Brammo style lower ball joints on front lower A-Arms. I think Brammo got this right.
Aero stuff:
-Louvered front fenders...reduce lift up front
-Similar molded seat, but with ability to remove the top rear portion of the passenger side (or ability to remove the entire passenger side of the seat). It would be nice if the seat sat even lower in the tub to get a lower CG
-Passenger side tonneau cover. When paired with side panels this would make the whole car more aerodynamically efficient & help with top end speed.
-Integrated winglets to span the tubes on the lower A-Arms up front...and turn turbulence into downforce.
I really think the Atom is just so close to perfection that most of the ideas I've come up with are probably best suited for the aftermarket.