The Alliance or Cerberus?

Cerberus. There would be no Shepard without them. and in me2 they're actually effective. The alliance can suck an egg

and Cerberus brought him back to life and augmented him with cybernetics which made him stronger faster and better.

once they were indoctrinated.

It's never said explicitly that he was likely indoctrinated long ago, but it is known he was exposed to Reaper tech during the First Contact War and his techno-eyes are based on Reaper tech.

Cerberus, they have drip and gorgeous women.

I'd prefer to freelance. Team Normandy. Shepard's a spectre who's got charisma and a large following of people who worship and follow them. There's really no need for them to be in the alliance at all. It's just more red tape. And I get sick of seeing Shepard salute those two stooges Hackett and Anderson. The alliance is pretty useless and Cerberus are recklessly stupid and untrustworthy. Shepard would be better off being a freelancer.

The Alliance is a bureaucratic dumpster fire of red tape, like our governments and militaries. Cerberus is what happens when bureaucracy and safeguards are removed: you get results but everyone is dead.

It's a question of what organization sucks the least for what situation. The Derelict Reaper is a perfect example: Cerberus immediately set up a research station inside the corpse and got the Reaper IF but everything as well as everyone was lost. The Alliance would probably set up an orbital station and spend the next few decades studying the reaper by using drones and might stumble upon the IF by accident.

And they get stuff done.  All Hail TIM

Since the Alliance wasn't getting stuff done, because they wasted 2 1/2 years, there was no need to fill out any paperwork. If they did, I wouldn't be surprised if the paperwork was put in a folder labeled Nothing got done.