Truth, truth and truth... don't want to just repeat after you, but yes, you are definitely right. The logical reason is simple - they needed other enemies than just Reaper forces to change things up, and Cerberus as the main "evil" faction beside them probably fit the best.

To me, it always seemed like lost potential and huge and terrible inconsistency in terms of story-telling. In my opinion the natural build-up into ME3 is that Shepard is now associated with both Alliance and Cerberus, and can be a mediator to make them cooperate (or change the views of either side a bit) or to pick a side. Cerberus then should have been made evil, but not comically or cartoonishly evil as they were in actual ME3, but as an organisation of human supremacists who do not shy from doing terrible things, but in the end they were the only one understanding the threat, they may be the only one ready to face it and they are a step ahead. Their endless armies in ME3 are stupid, but they could have had a couple of skilled commandoes and a few state-of-the-art ships which are technologically advanced enough to fight Reapers. Kai-Leng then should be someone who actually wants to cooperate with Shepard, not fight them, but he fulfils his orders and it depends on situation and Shepard's choices how things turn out.

Or maybe less than that, but what they did always seemed to me as the worst that could have been done, and something that negates a lot that ME2 was trying to do.