There is ultimately no comparison in depth: 3rd Strike wins, hands down.
Now, bear in mind, Mark of the Wolves was designed to emulate Street Fighter III in style of animation, speed, feel of gameplay, and even the controls. (It breaks SNK tradition by adopting the "simple" super move commands like SFIII - virtually all supers are a quick and easy motion, easy to combo.) So at first glance, they're going to seem really smiliar.
MotW has good depth, mind you, especially if you master Just Defense and other skill-based techniques. SFIII however just has that much more - if you keep plumbing the depths, you'll find more. More moves, more possible interactions between fighting styles, more strategy with positioning and timing, the parry system being deeper and opening up more possibilities than Just Defense.
Aside from pure gameplay, it's going to be about aesthetics. 3rd Strike has a bigger cast and IMHO, a better balance between styles of fighters. I also feel it's more balanced, overall. And even though there are a few Shotos in it, it still has a great variety of play styles. MotW has more SNK-ish character designs (duh!) and obviously many folks will prefer those to Capcom's more "basic" character concepts. Though personally I feel 3rd Strike is the most SNK-ish of Capcom's SF series in terms of character design.
Otherwise, graphic nod still goes to 3rd Strike by a little bit, and musically, I think the music in 3rd Strike is a league above that in Garou.