Let me explain.
I don't actually like antagonists, I dislike them for obvious reason - they are antagonists. This rule works for me with only one exception. I like the antagonsits who have noble goals, but I still dislike them for their choice of methods. It doesn't matter The Catalyst was introduced in the last 20 minutes of the game. What matters is its noble goal, unacceptable method of achieveing this goal (cycled harvests), and the scale of its influence. Besides, this character's existance was completely unpredictable till the very end, and provided very interesting turn of events. And when in the end we start to understand that according to the story The Catalyst's methods led to the birth of Humanity, Asari, Turians, Salarians, Krogan, and so on... This is why The Catalyst is probably my favorite antagonist of all times. It as much creates life as it destroys it, like our dear mother nature.
The main issue I have with the catalyst isn't so much what it's trying to do, but rather the reasoning that it gave to us as to why it's trying to do it.
Part of the problem is that Mass Effect 3 is all about unity. We're all coming together to fight the Reapers and the entire game is pretty much spent in getting everybody to play nice which includes the Geth and the Quarians, a conflict that was started by the organic Quarians.
but then suddenly star child shows up and goes "Nope. Machines and organics can't work together. The organics will just get slaughtered" even though I just made peace between machines and organics with the Geth/Quarian thing. There's very little explanation offered here and it ultimately comes off as a "I'm right you're wrong lalalalalala I'm not listening" kind of argument.
There's also no talk of potential other solutions beyond Reapers and the Crucible and no explanation as to why the Reapers were the best available solution at the time.
He might have worked better as a character if they didn't introduce him in the last 20 minutes of the game because he would have had more time to get dialogue in so that everything could have been explained better(even though it technically was supposed to be a thing we could not comprehend =P) rather than being left with what seemed like the most illogical AI ever created. Even with the EC, I think that the Catalyst just didn't get enough screen time in order to be given the chance to develop into a good antagonist.
I'd also make the argument that the Catalyst did not create life as much as it gave it room to advance and evolve. Even without that, one can't entirely make the argument that the species of our cycle 100% for sure wouldn't have advanced without their help into whatever galactic community they had, either better or worse.