As far as sympathetic villains, there really aren't many, which is a bit disappointing to be honest. Too many of the villains seem to be evil for the sake of being evil (I'm looking at you Apostate and Gloomweaver).
In addition, many of the villains have very flimsy and petty excuses for being evil. Both of Tachyon's nemeses, Friction and The Matriarch, are so petty it's pathetic. The two of them are essentially just throwing tantrums over imagined slights, and are completely unreasonable and childish (at least The Matriarch has the excuse of actually being a teenager). I was kind of disappointed when I learned Ermine's backstory, given that she is clearly the Catwoman to Wraith's Batman, and yet lacks any of the redeeming qualities and character depth that Catwoman posesses. She too seems childish and pathetic.
Iron Legacy is not all that sympathetic. Sure, I feel bad for the poor guy, no one should have to watch their own child die, but that certainly doesn't justify his reaction. I can't blame him for killing Baron Blade, but his regime of terror? That I can certainly blame him for. Yes, his daughter was murdered. Baron Blade's father was killed by Legacy's father, that doesn't make Baron Blade sympathetic, and the excuse isn't much stronger for Iron Legacy. I actually found the idea of Iron Legacy kind of disturbing, it's frightening to think that Legacy was that unhinged, that unstable.
Miss Information is sort of sympathetic, but not really. She's a victim of the overlapping timelines, but her reaction is still over the top. The woman is clearly very intelligent, she could have gotten work wherever she wanted, yet she chose to assist the Sentinels. Surely she must have been at least partially motivated by a desire to help others, and yet here she is trying to murder the people she worked with because in another timeline they let her die. I can't really sympathize with her.
Plague Rat is actually one of the more sympathetic villains. He's a victim of circumstance, was probably poor and almost destitute before his transformation. Sure, he was a drug dealer, the guy was also homeless, he wasn't exactly a drug lord, he was just trying to get by however he could. And now he's been robbed of his very humanity, become a mindless beast, living in a terrifying world in which he can't coexist peacefully. Hard not to feel bad for the poor guy.
The Dreamer is also fairly sypmathetic, again, a victim of circumstance, and clearly not really a villain, just a victim of her own powers. Not sure it's even fair to call her a sypmathetic villain, she's not really a villain at all.
One of the more sympathtic villains in my opinion is Fright Train. This guy is the victim of an uncaring society. He's a veteran, who nearly died serving his country, and yet when he returns home, he can barely find work and realizes there are next to no opportunites for him. He tragically makes the mistake of embarking on a career as an illegal mercenary, using the skills he has to try and make a name for himself, to carve out a life for himself. And in return, he gets experimented on against his will and subsequently locked up in an extradimensional prison. Plus, the fact that in the Iron Legacy timeline he has taken up the mantle of Bunker suggests to me that he really is a decent guy, just misguided and frustrated.
Lastly, I kind of wish we knew more about Akash'Bhuta. She never speaks, so we have no way of knowing her motivations. She may simply be lashing out at society for the way we have been systematically killing the planet for thousands of years, in which case, can you really blame her? But unfortunately, we have no way of knowing that, and so she just seems like a mindless monster.
That turned out way longer than I intended. I have always loved villains in movies and games though, so it should come as no surprise that I feel strongly about this sort of thing I suppose.