She cheated on her husband, broke up the royal family, undermined diplomatic relations with other kingdoms, clearly didn't give a shit about her people or duties, and created highly dangerous magic that is, if not innately evil, at least morally suspect.
Eclipsa's problem is that she fundamentally doesn't care about anything except what SHE wants - which isn't an attitude you can have as a ruler, and is something Star should have called her out on. No, she's not wrong to love a monster - but that doesn't mean she should still be queen, because she was a TERRIBLE queen who manifestly didn't give a shit, in direct contrast to Moon and Star.
She should have just abdicated, and Star's development should have been resolved with her feeling more secure about the fact that even if she's not as powerful or confident, she does actually try to be better - and has been trying for about three seasons.
Also, the whole Meteora arc should have been resolved deliberately, with Star and Marco working out that the only way to have a "happy ending" would be to literally undo her awful life, and using Princess Turdina's influence to overcharge the princess-draining machine she was using to STAY YOUNG.
Instead of her just beating everyone until Eclipsa beat her and then wow how amazing she's a kid for some reason, ignore all these guns that Chekhov left lying around.
Season 3 was a mess.