Personally I feel Sun God is now his best. I'd say sun, then war, then blood, but that all three are viable.
I think sun is the best because there's no range where he has no options. War can still get zoned out, but with parry and sun charge, sun can deal with zoning while making the opponent not even want to zone. Midrange, all the Kotals now have safe options and a real antiair grab, so war god's ability to end strings in df2 for safety is less important, although still good. Sun's command grab mixups are no less safe and in some situations safer than war god's overhead and low. F12 being safe really opened up the command grab imo, since it gives a credible tool in midrange/pressure that opponents have to respect on block more. The grab/not grab mixups also lead to more damage more consistently than war overhead/low mixups imo.
That said, war still has extra safety in strings, controls more ranges, and has better wakeup attacks, and those are all important.
So I feel sun is more versatile, but it's also a matchup thing. Where Kotal wants to get in, I think sun is better. Where Kotal needs to control space and have good armored moves to escape bad situations, I think war is better.
All that said, the one I've actually been playing most is blood heh. I agree with the posters above about the improved totems being good and parry making anti-zoning more viable. In fact blood might have the best anti-zoning options for Kotal. On one hand, putting up a crystal and parrying a fireball makes your next ex sunstone do ridiculous damage on hit or block, and the opp has to respect the danger of trading. On the other, putting up a defense totem means you can walk and block or parry and not worry about the chip or mistiming a parry and eating like 4%. It's also just really fun to make decisions about which totems to use when. Getting good at it is hard but there's a really high ceiling there imo! Too bad about blood's lack of mixups, but with faster b1 and safe f12 Kotal can make some pretty credible frame traps, and blood god can capitalize on them like no other.
Anyway, I see sun and war as being legit contenders to win a major. Blood god I'm not sure but I think it can make real top 8s. Kotal is good!