My personal opinion : Yes, they are. DmC Vergil battle is a complete cakewalk even on DMD (well, the whole game is a cakewalk tbh, but that's not the primary topic here), whereas in DMC3, the first Vergil battle I consider to be easy, but he still hits harder than DmC Vergil. 2nd Vergil battle is my personal favourite, it's a good challenge (way, wayyyy harder than DmC in general) and is really fun to play, while also having a great music track. The third battle is harder than the second (it's actually very hard to beat him on DMD unless you have practiced the battle ALOT) and is very fun as well, I do like the second one a bit more though cause there is a bit less "CRASH! BEGONE! CRASH!" spam which you have to dodge haha, although it's a good challenge for your DMC evasion skills and is still fun.
TLDR: Yes, DMC3 Vergil battles are better than DmC, they are both more challenging and more fun.