Er, no, ME2 basically portrays humanity as the Only Hope the galaxy has. We are so good at the game that a human terrorist group can single-handedly save colonies, face the Reapers' minions and succeed.
Cerberus is an incompetent gaggle of failures. Literally, everything they do apart from (i) building the Normandy v. 2; (ii) creating EDI; and (iii) reviving Shepard is a total failure. They're such failures, actually, that you stop the Collectors literally without them, because they're such dead weight they can all get kidnapped without even slightly affecting you (thanks to, again EDI).
The most competent part of the Normandy that isn't (a) Shepard, (
Shepard's squad of elite non-humans, or © Joker, is EDI, the former mostly Reaper AI.
Everything Cerberus does is a total failure that Shepard has to clean up. Their actual crew is basically useless filler, rendered redundant by EDI. And EDI isn't really a human achievement - it's a synthesis of Reaper technology and a failed human AI that Shepard - again, the ubermensch saviour - murdered.
And look at Shepard's squad - apart from Miranda and Jacob, it's all non-Cerberus humans or aliens. And even the absolute best humans are not as good as the random aliens. Our brilliant scientist is Mordin, a Salarian. The most powerful human biotic in existence - by far - Jack is basically equal to a random Asari (because, lore-wise, there's nothing unique about Samara). The other hypercable tech genius is the Quarian - Tali.
Miranda, the super-human genius designed to be better than humans at everything, is basically as good as Garrus, a highly capable but otherwise not particularly distinctive Turian.
"Humans" don't do jack **** in ME2. Shepard the ubersmench does, but the elite carde of humans he has are barely as good as the grab-bag aliens with the team.
What it isn't portrayed as hypercompetent anymore isn't humanity, but the Alliance. There's a very important difference, and part of Cerberus' slogan. The moment human higher-ups start becoming as complacent and bureaucratic as the rest of the alien powers, only Space Jesus and those who keep alive the "ubermensch innovators" idea can save the galaxy, because the rest are useless. Then add the genetic nonsense and it's basically canonized as "we are special because the Universe says so".
The Space Nazis who resurrected Shepard and helped them save the galaxy in ME2 while the rest of the alien powers and the Alliance were too useless to do anything, and who brainwashed as they were, were able to be the main enemy during the Reaper War after the Reapers themselves. If anything, it basically says that "even our terrorist groups are better and badder than yours, it's just that they are terrorists and of course they have to fail. Put them under a hero and they will be able to do things that whole galactic powers can't".
But Cerberus is totally incompetent. A huge part of the game is about their complete failure - Overlord or Jack's backstory come to mind - and even their supposed "achievements" (like the Derelict Reaper) only play out because Shepard is superhuman and is involved.
Cerberus fails far more fundamentally and comically than the Alliance. The worst you can pin on the Alliance is that they don't believe Shepard's obviously insane rambling, which despite how hard the story wants to tell us is an issue, really isn't all that strange of a reaction. And that's not even all of the Alliance - Councillor Anderson tries to do at least as much as TIM, and the heroic mission in Arrival that ends up buying 6 months to find the Crucible
all happens out of a favour for Hackett.
The Space Nazis don't save the galaxy - Shepard does. The Cerberus Crew with you - apart from bullet sponge Jacob and Miranda - are completely useless and rendered redundant by EDI. Cerberus itself, as an organization, doesn't do much of anything apart from give you intelligence and a bunch of resumes.
And even Normandy v. 2 is kind of a piece of **** without all of the alien innovations that get added to it.
As for ME3, that's not really a human group anymore. They're a repurposed Reaper attack team, and even racist imperialist Prothean Jim tells you they dealt with the same crap in their cycle.
Cerberus is one of the biggest failures we see in the series. It's only the arble-garble political logic of the writers, and this idea that rich industrialist love to finance secret mad science out of their personal wealth, that even allows Cerberus to exist.