|Don't get angry. Get edited. Then maybe get angry.|
A competent editor is a liaison between the writer and the reader, making sure that what the author meant to convey is what is actually on the page. We are there to make you look as good as possible. A competent editor does not make changes unless they serve the interest of the story, and should be able to justify every change. If an editor makes a change you consider ruinous to the story, STET THAT MOTHER.
An editor's changes are not decrees carved in stone. Authors can contest them, and the editorial process should not be over until the author and editor agree on all points. I've had authors contest edits I've suggested; it's all part of the process. Sometimes, with explanation, the author realizes that what I've suggested makes the story stronger. Sometimes, the author's explanation makes me agree that their original version was fine.
If you've got a contract that doesn't require the publisher to get your approval on substantive changes like removing a whole section, that's a bad contract no matter who is editing the book. As far as cover art, the publisher is wrapping the book in something that it thinks will make people buy the book. Ideally, that will accurately reflect the content of the book, but that's not always the case, and where the two interests diverge, marketing takes precedent over accuracy. There are persistent, problematic biases with cover art, not the least of which is whitewashing characters or sexualizing female characters regardless of their actual role in the book. That needs to change, but it's not the editor's doing, and in the end it is all about getting your story into the hands of more readers.
So, for the tips:
1. If you're engaging a freelance editor, either for a self-published work or pre-submission, shop around for one whose style matches yours. If your editor firmly doesn't believe in prologues and you write lots of prologues, you two are not a good match. Keep interviewing until you find one who is.
2. If you're working with a small press publisher, you may be able to suggest they engage your preferred editor for the work. The small presses I know of have a stable of editors they go to, but they essentially contract the work out, and may be amenable to contracting to an editor you suggest if they can be assured that the editor meets their quality standards.
3. Engage a competent editor. Competent editors don't make changes for the sake of making changes, or to pee in the corner of your manuscript so everyone knows what a terrific editor they are.
4. Realize that the editor is working for the good of the story, and the reader. Editors would just as soon not incur the wrath of an author, because cheesed-off authors are difficult to work with and we have limited time in a day. Edits are not personal. Related: 99.2% of writers do not crap gold on either first draft. Or third.
5. STET. STET. STET. You do not have to accept the edits. If you are contractually obligated to accept the edits, get a better contract next time.