A few nice tweaks to wake up kicks would be to get rid of the high, make them unsafe on block (both mid and low), and have them NOT stun on hit. Slight disadvantage or even neutral would be fine (unless it is a CH of course, in which case advantage would be preferable over a full stun). Also making them linear would be nice so players could have set ups where they could sidestep them and get to the opponent's back and punish them for trying to do the wake up kick.
I'm also with Chris about the NH launchers. Moves like Bass p+k, Hayate 8p, and Ayane BT 6p (boy would I love this) should be NH launchers to either use as block or whiff punishment. If Bass could do p+k to block punish, get a ground slam, and a free pick up, that would give him viable options in situations that he did not have in 4 and even 3.1 since p+k was not a NH launcher in that game either.
In DOA4, if a player whiff punishes with Ayane's BT 6p, all they would get is a stun. If they do a launcher right away, they risk being held for only a minimal launch height. From what it sounds like, this situation still exists in DOA5, and is something that is hopefully addressed in the final version. Just because a launch would be full height does not make up for the fact that the launcher would be holdable in the first place.
I also like the system they had in 4.0 where some strings were 3-in-1s or 2-in-1s on crouching opponents. Ayane 3pp (with a full or decent launch), Busa's 3ppp, and Zack's 3ppp would add to the game without adding more counter hold situations. Even strings with nice range that are unholdable after the first hit on NH would help the whiff punishing problem. Ayane's kkk* (not sure if it's different in the demo) would be a nice way to block and whiff punish without worrying about holds. Make the strings unsafe on block or end in highs but hit confirmable (or safe after the first few hits) and it would add some of the depth we want from our game.
*Sorry for so many Ayane examples, but since I'm an Ayane player examples for her are easier for me to come up with.
Having the stun system is fine, as long as there are ways to work around it; with special stuns that don't allow holds, NH launchers, and strings guaranteed after the first hit, the game could make great strides towards being a great fighter. That was the strength of 3.1. A player could formulate an effective strategy by limiting how much they would risk putting their opponent in a stun. The problem though is some of it was based on getting a CH, and the hold was still a big part of the game because certain strings could be held on reaction which would limit their usefulness.