For another, the Catalyst is supposed to be the antagonist. The enemy. Why do people want him to have as friendly a face as possible?
Because he's an antagonist does not necessarily mean he has to be the enemy, or even a villain. You're stating what you want. Other people might agree, but this is on your own ideal. I disagree about the VS being the avatar; for starters, how the hell would the Catalyst even know about the Virmire Death?
That said, there's nothing wrong with a supposed God-tier antagonists. The Reapers are not villains to be vanquished, but opponents to be outmaneuvered and defeated. I have no hatred for them: They're following their mandate. I disagree with it and hold it to be full of logical fallacies and inadequate science guided by a breathtaking god-complex.
I believe the Catalyst should make a unique style of appearance and position, being an utterly alien and unrecognizable being with its own unrecognizable sense of morality and ethics. It doesn't play by our rules, and we don't play by its rules. But to simplify the conflict, its a legitimate conflict of interest. It does what it does, and I do what I do. They're incompatible, thus bringing conflict. One lives. One dies. However, you can have a programming error in the hardware that makes it feel that it does what it does out of a logic bomb. That's how I view it already. It's too limited in its mandate. Too much emphasis was placed on its logic, and not enough placed on its end-state consequence.