This si the first DOA I've ever owned, so I can't really compare it to the other games in the series. BUT, throws seem to work pretty well, yes lots of low hits pass over grounded opponents, and apparently the window for counters has been drastically reduced (by almost half I've read) although the computer seems to have little difficulty countering if you do the same attack more than once.
All in all, it sure does look pretty. Plays pretty well too. Computer can get pretty irritating with it's constant juggles and counters in later fights, but I've beaten it with a couple of fighters (Bass, Ryu). Haven't unlocked Spartan-458 though..