Total War and Warhammer Fantasy are made for each other. The two games flow similarly as far as movement and morale mechanics, and have similar unit sizes.
Warhammer 40k is almost a small scale tactical game, though you can throw hundreds of models on a table. There are Warhammer 40k spinoffs that would work in a Total War context, but it would be more Total War than Warhammer 40k.
Great news! The Total War series was obviously inspired by the two classic Warhammer games (of course, I'm talking about the immaculate Shadow of the Horned Rat and Dark Omen), so it's great to see it come full circle. I have faith that this is going to be quite a bit better than Mark of Chaos.