A compiler or similar tool doesn't generally affect the license of its output (some of them explicitly disclaim that), just as a text editor doesn't affect the copyright of a novel written in it. The GPL is much more widely popular than the EPL, and now that it contains comparable patent language it is probably a better license to use (when the EPL was first written it was primarily to address patent issues that the GPLv2 didn't cover). I would hope that projects that are using the EPL would now migrate towards the GPL where possible - strong copyleft licenses are inherently impossible to combine, so it's best if the community can standardize on just one.

The MIT license is compatible with almost everything - it's really very minimal, comparable to a 2-clause BSD-style license. There is no problem combining MIT licensed components with EPL licensed components, or with GPLed components. (Of course there is still a problem if you want to combine with both at the same time)