CoC2 has party-based combat (which I'm always a fan of) and the way it handles standard (i.e. gender, racial etc.) transformatives is much better than in TiTS, mainly because they're standardised and can easily be targeted to specific body parts. TiTS is more technologically advanced (which I consider to be usually a good thing) and has a much greater array of specific/unconventional transformatives like SnakeByte, Nuki Nutbutter and the various illegal TFs (CoC2 only has Bimbo Brew). I have no real preference for energy-based vs cooldown-based combat, though I tend to use powers much more in the latter system.
In terms of societal issues, I consider TiTS to be better overall. While it does have indentured servitude which can be abused in such a way that it's effectively slavery, such abuse doesn't seem to be the norm (or at least, it's definitely not the only way it's done) and slavery proper is illegal throughout the UGC; meanwhile, CoC2 has legalised slavery not just among the orcish (read: barbaric) tribes, but in powerful central nations like Jassira.
Racism in TiTS is quite rare in the UGC (at least when it comes to humanoids) and is almost always portrayed as bad or otherwise unsympathetic, while in CoC2 it's much more commonplace and some portrayals seem to be closer to neutral or mixed than outright bad; you're also much more likely to find someone who doesn't fit their race's stereotypes in TiTS than in CoC2 (I'm looking at you, kitsune den and Mallachite temple!).
The UGC also has a standardised process that allows newly-discovered races/societies a chance to join them as equals rather than be subjugated or destroyed; CoC2 has no equivalent. As far as I can tell, they are otherwise quite similar, particularly in regard to sexual issues (mainly a lack of sexism, homophobia, transphobia and the like).
On the matter of their protagonists, the Champion is a generic blob some random person who happened to be in the right place at the right time and could be replaced with pretty much any other random person without affecting the story, while Steele is much more well-defined and their story doesn't work if they're not the child and designated heir of Victor Steele. I much prefer the latter and think it makes for a better story, but maybe that's just because my experience with RPGs is BioWare-dominated (their protags are typically more well-defined than those of other RPGs).
Overall, I'd say TiTS is my favourite.