I think it's really up to personal preference but since I went Engineer primarily I dumped most of my initial certs into the nano tool and suit mods, before saving up the 50 to cert AMS. I then used some on reducing sundy cool down and tweaking the weapons with ammo capacity and zoom optics.
my next 50 will go back into the nano tool and then I'll start adding tweaks to my weapons before going back to adding mods like repair and re-arm to the sundy.
For support roles like medic and engy I spend points on the nano tools and abilities first because they will help you get cert points faster but If you are playing a combat role then I would start by putting points into suit upgrades to help mitigate damage and weapon upgrades.
I looked at it as a class specific skill tree like in a RPG, think of the Heavy assault as a tank class and the light assault as DPS and Engineer/Medic as offensive and defensive healing classes.
You can kind of think the same way if you choose to run vehicles most of the time.
I'm not really sure if that sounds crazy or not now that I read it back to myself.
Points come a lot faster than they did in beta so you can probably just spread them around however you think will be the most fun.