About Trandos on the RAS:
They were probably aided by the Separatists. That's where they got all the droid hardware that they usually couldn't afford, like all those Super Battle Droid Dispensers.
About Clone Troopers:
Yeah they're way to weak. They really shouldn't have dumbed them down and they even made that first one you meet on the RAS a traitor. It would have been nice if you could have commanded those Clone Troopers on the RAS to follow you, move out, heal themselves with bacta, etc. There's really no point in even helping them other than you feel like a good citizen.
Considering that the Clone Troopers in RotS are going to kick even more ass than in AotC, with the Jedi extermination and all, it's going to make Republic Commando's interpretation of the troopers look even more off.