Not necessarily my most picked, but certainly my favourite in order of perceived greatness:
#1 Juggler. It's just amazing. At level 2 you can get a skill that makes you the most adaptable marine you can get. It's like it's your own little "get out of jail free" card with the ability to whip out a RL whenever you need to or switch to your DB shotty for close range. You also become an absolute gun ammo platform with this skill, dual wielding combat shotties or plasma rifles (even without MAc that's plenty of ammo). It even beats shottyman for shotgun usage but is still useful with any weapon. The more weapons you have, the more it scales, so it gets better and better as you go deeper into the game. It's almost at the level of a master trait in terms of usage and you get it so early. It is that good.
#2 Badass. Just for the synergy and the lovely passive defense it offers. You've already got an extra two armour before you get this, so why not have more health to round out the "will-not-die-factor"? It lets you collect those health globes pretty much whenever you want and scales nicely with the inevitable ironman levels in late game. 160 health and +2 armour? Yes please!
#3 Whizzkid. It used to be good for a lot of reasons before. Modding, backpack space (to use up "useless" mods) and it was on the way to Mac. Now in 0.9.9.2 it's even better with assemblies. And it will probably get better still as new versions are released and we get even more advanced and master versions of them. But still, who doesn't want the biggest gun, the spiffiest armour and the sparkliest shoes they can get as they trudge their way through hell?
I've actually been playing a bit of AoI recently and I'm finding I can't rely on a master trait build or even a good no-master-trait trait build very easily. But advanced trait builds rock. Going for something like Fin->Jug->Fin->WK->Ir->Ir->BA or Fin->Jug->Ir->Ir-BA-Fin-WK scales so quickly and is so good that the build is over before you know it. You either grab WK early if the mods are kind to you and special levels spawn nicely, or go the passive build and mod out near the end. The build also performs brilliantly in a full game except you still have usually another 3-6 levels of traits up your sleeve before destroying cybie with a barrage of BFG, rocket and plasma fire. Juggler FTW :)