There are only two times I found that DMC3 felt "clunky" (for lack of a better word, since I'm not sure I feel it quite the way you do, OP)
1) The very first time I played it, in which I quickly got over it.
2) Any time I play it after a prolonged period of not playing it-in which I re-acquaint myself with the controls.
I will admit there are times it feels kind of stiff (for me it's because I got so used to the fluidity of movement in DMC4-and yes, I'm talking about both Nero
and Dante's moves), but once I get back into the groove of things, it's probably by far one of the best games I've played in a long time.
(I'm a pretty selective gamer; there are only a handful of games that I get replay value out of; most others I'm done after a single run-through).
All in all, to each their own. Play whatever you prefer; if DmC feels better to you and you enjoy it more, go for it.