Presumably the CTO got a lot of the existing codebase into place, and in a rush. If the flipside of that is that the company has a successful product which is attracting customers and investors, he had his priorities right.
There is a chance he'll get defensive and attempt to rationalise his decisions. The odds of this go up if you're confrontational about things.
He may also think he's right on some fronts. He could be right on some fronts. If every engineer in the company is using Eclipse, is it really a problem that people haven't spent time making sure the codebase compiles outside of Eclipse?
I would advise you to be open about the way you would do things, and to do things that way if you don't encounter opposition. Getting argumentative and/or getting into commit wars is unlikely to help your cause.
(If you want to keep your job at all costs, shutting your mouth gives you the best odds, especially if the CTO really is a dick. But it doesn't sound like that's what you want to do).