I'm at work now so limited time to reply, but this is a great post that re-focuses attention on the key issues, so kudos

I knew there was potential derailment discussing SC comparisons, which I will follow up elsewhere, but for now...
I don't play Brad in VF, so I couldn't tell you his frame data, but when Zack does PP2 to get into Ducking, if the PP was blocked, Zack was at -25 in the E3 build. That's a free punish. There's nothing to read about that. I see Zack do PP~Ducking, I punish him. Simple as that. Zack can't do anything about it.
If Zack can be punished anytime he goes into stance off of a blocked attack, there's no point to the stance. Same with Helena (referring to DOA4), same with Brad (referring to DOA4), same Rig, same with anyone else with a stance.
If you want to compare this to VF, let's compare. Almost every time Lei-Fei cancels into stance he actually has BETTER frames than if he didn't cancel. It's designed this way so that the Lei-Fei player has a reason to go into the stance. If Lei-Fei was punishable every time he transitioned into a stance, Lei-Fei players would never use his stances.
Very good points that addresses the specific issue of why and where frame advantage is needed; so you can actually play through your string, or transition to stance. (Not to end your string and get something for free necessarily)
The mind game intended is the same for Zack as it is for Brad, you are varying your attacks to fish for a counter hit or just keep the pressure up. Thank you for pointing out that Zack is at such disadvantage going into stance - that is definitely an issue.
There is a caveat, and that because he is ducking, he can't be hit with a standing throw, counter hit by a jab (and does it duck mids? I can't remember exactly), but that level of disadvantage, if the opponent is watching for it, means a low throw punish. The thing to double check is whether the low throw will be beaten out by Zack's PP from ducking, because blows will instantly beat throws in DOA and that system will work for him from here.
So yes, as I said - I tend to agree with what you identify as issues and on the solution even if I don't always jive with the comparisons used. This is very clear, however.
That's not to say all stances are completely safe or at advantage, for example I play Pai and her Bokuho stance is fast to get into, and is low thus evasive (sometimes dependent on distance). It's what you do after Bokuho that determines if you are still safe or advantage or not (and where a form of guessing comes in). If Zack can be punished going IN, rather than executing FROM his stance, yes there's an issue. If he has enough time to start his next attack, he'll be fine (cannot be low throw punished).
The difference in the Bokuho example is, I might be safe going into bokuho and can begin executing my attack, but the reads are thus: If I sweep with K, they can't evade or attack high, but can hit me with 2P or low block and punish. If I P+K they can evade or interrupt with 2P and we're both at neutral/slight disadvantage to me.
If I know they will 2P I can G+K and hop over for a combo. If they standing block, I'm at disadvantage and can be punished.
So its still a guess and I don't necessarily have advantage, but I DO at least have time to make my play. That's all I'd expect from Zack in ducking stance and its a really small tweak to his frames would ensure its not actually unsafe just to go in on a blocked PP. That's the kind of frame advantage DOA needs at minimum.
We aren't even discussing the counter. It's not changing and I've accepted that.
That said, counterholds are toned down from neutral, but they are virtually the same during stun as they were in DOA4. In DOA4, if you were expecting the opponent to counter mid-stun, you could punish that counter with a throw. It wasn't hard to do. The shorter active window and longer recovery do not change the fact that an opponent can spam a counter over and over in stun. It doesn't change the fact that low counters evade high attacks. It doesn't change the fact that the counter executes instantly.
I agree, the low counter is still a problem. The i0 execution is fine as you still have human reaction time keeping it practical and the real issue is recovery and fear of punishment. So the low counter evades highs which gives it dual purpose and that's a little too good. They aren't likely to change all the animations to make it LOOK like they reach down from standing and therefore feasible to get hit by a high attack.
But they CAN extend the recovery on lows to ensure its possibly for an attacker to whiff a high jab then still punish or at least have pressure advantage. That's definitely a reasonable recommendation we can make.
There's a difference between wanting to get more out of a situation by guessing, and a situation in which you are forced to guess every step of the way. DOA forces you to guess all the time. You don't have an option. You have to guess or you will lose. In no other fighting game are you forced to guess. It's always an option, but never required to win or be skilled at the game.
I don't quite agree with this - you can play safe when you attack using distance and specific moves, and block more than you counter when you defend. Even in DOA4 this was viable if you look at how Offbeat Ninja played. His was not a guess heavy playstyle.
Likewise you ARE forced to guess particularly on defence in other games - are you more focused on the attackers options in this discussion?
There is more variety available to players while still being more safe and guessing less. I know you feel delayable moves cause guessing, but it actually gives the attacker more advantage once you work out where and how the opponent likes to block, if you don't have time to throw punish or think they'll tech crouch, you delay a mid. I do this in VF too.
Ultimately I think the issue of moment-to-moment guessing, while we differ on this a little, I think we can agree that the frame advantage and recovery issues discussed above will naturally address much of this.
Then you have your sit downs and Critical Bursts to play to. Kind of like how in VF you tend to have to get a counter hit, or a wall hit, to land a big attack like a re-stand. Then you go to town. CB's will allow that in DOA5.
Where is the rule that states no mid launchers can tech crouch? How does a tech crouching mid launcher stop me from reading the situation and reacting accordingly? VF has ducking, mid launchers. Tekken has ducking mid launchers. DOA even has ducking mid launchers.
And I'd much rather have a game that requires the opponent to know what my character can do instead of knowing general system knowledge and using their intuition to win. I don't know any fighting game in which "intuitive game logic" is enough to win. Even in DOA4 it wasn't enough, and the game logic of DOA4 was nothing like the game logic of other fighting games.
To avoid derailing further, I'll post another thread and edit a link in later.