Not every move needs to have an effect. Some moves can just deal damage on contact (or naturally combo). Not everything needs to stun or knockdown.
The reason why some don't like stuns is because of the ability to hold out of them. I've already posted something similar elsewhere in the thread, but I'll paraphrase. Let's say I get through your defense and I hit you with something that stuns. Instead of just you taking that damage and me being able to punish you further, I instead have just put you in a situation where you have the ability to guess out of the stun using a hold, effectively ending my offense if you guess correctly. Not all stuns are holdable, but a vast majority of them are. In DOA 2 and 3, this wasn't as big of a deal since there was no stun threshold, there were more natural combos, and there were a lot less stuns overall, meaning you had plenty of ways outside of stuns to get your damage. HCH throws also did ridiculous damage, so it actually made the defender scared to guess with holds. DOA 4 and 5 decided to place the emphasis on this stun game, and as a result they increased the amount of stunning overall, thereby creating more situations where the defender has the ability to blindly guess. They also slowed down the stronger throws in the game, effectively making holds harder to punish. Some people like this new guess heavy system since it practically gives them a second chance to get themselves out of harm's way, but a lot of other people are irritated by it for that exact reason.