Chrysalis currently holds the distinction of being the only true villain the series has left... Nightmare Moon was redeemed and restored as Princess Luna, and Discord promised to behave so he could stay chummy with Fluttershy, while Sombra was blown to bits. Anyone else pretty much just qualifies as an antagonist. I wonder if we'll get any lasting villains coming out of season 4.
The desire to have antagonists reach redemption seems to be pretty strong with the show, at least among a large chunk of the fandom. I know of plenty of efforts to make Chrysalis herself more sympathetic as well. Of course, I've already gone on record as liking some nasty characters, and I'm quite happy having changelings being monsters... but then, I'm old enough to like my vampires evil, undead bloodsuckers preying on innocents and not misunderstood romantic characters. I figure there's room enough for everyone's favorite take though.