i pretty much just upgraded what i could afford (my guy is a positive karma guy). i was so into the game that i kept forgetting to upgrade. lol so when i'd finally remember, i'd have 5000 xp to spend and just do a few, whatever i could afford.
but the obvious good upgrade IMO is the lightning bolts and the quicker charging. also, for the fun factor - the drop upgrades. nothing beats thunder dropping multiple enemies when they have no idea they're about to be owned

although... i've found that they detect me and start shooting as soon as i jump off the building, which is ok i guess but sort of unrealistic. i don't know about you guys but when i jump off buildings onto a group of bad guys, they don't hear me coming.
(spoiler)
i just got the precision shot unlocked, but i was disappoint to see that it takes up 4 dots per shot. that's too rich for my blood.
also, riding the rails / power lines and being charged simultaneously is pretty cool. you get around quicker, and charge while you're at it.
i love this game. i'm gonna play when i get home.