ToV's main villains are bad, though some of the earlier villains (Yeager at least) are interesting. The fun part about ToV is seeing Yuri and Flynn's differing perspectives on solving the (admittedly-poorly-planned) machinations of the main villains. Rita and Estelle round out a really good cast, and even the less-amazing PCs bring -something- to the dynamic.
Yeah, there are some half-decent villains in ToV, but the primary faces are awful. in Yeager's case, though, he's pretty bland until his very last scene which puts him all his motives into a whole different perspective. Its a neat touch, and well done, just of course the issue is if you don't get to that scene, it is really hard to understand the hype (well, ok, he's got a unique accent at least), as he comes off as a generic scum-bag otherwise.
I would also argue that TotA at least has a good set of mains in Luke and Tear, and hopefully Fenrir at least got far enough into the plot to see how they were developing before skipping everything... >.>;;
Yeah, I think most people, even the TotA haters, agree that, at very least, Luke and Tear are well done. Just TotA has an issue of having far more questionable characters in its cast. I mean, of the primary PCs, the worst ToV PC is...Judith, I guess? And that's more a "by default" thing of the other characters being better, rather than her actually being bad.
Flipside, as has been shown in the past, Anise is...less than popular...to say the least. TotA does have the Fun Master admittedly whose pretty cool, but ToV's not without its good NPCs (Flynn comes to mind) so yeah.
...and I just realized that Flynn and Ion are pretty much each game's respective counterparts. They both basically serve the role as being a foil for the main character, and they're both actually pretty good at their job too (Flynn I find especially impressive, cause DESPITE having a majority of CLICHE SHONEN RIVAL traits...he manages to subvert the trope rather well by sidestepping some of the major plotholes these types, regardless of where they started, fall into. I think the best example is how they handled in the inevitable duel later in the game)