I notice that you seem to refer to 5A as the "poke" move, so I will clarify my terminology here to avoid confusion.
Poke = (using) any move in an attempt to land a hit or pressure and/or condition the opponent.
Point 1: Health and Damage
Preferring Farther range = less damage, closer range = more damage
1 hit = 1 damage
Adding variable damage per move does not change the fact that being closer will give you higher damage combos. What it changes is their value as standalone pokes during the neutral game which is one of the big concerns that myself and others share.
Let's say for example Tenchi's specials do 2 damage per hit, his A buttons do 1 damage, his 5B and j.B do 2, and his 2B does 3, like I described before. Let's also say that jumping doesn't beat lows and will actually get caught by them. And finally, let's say there's no damage scaling at all.
This makes Tenchi's 2B much more useful as a neutral game poke and more useful to punish jumping while still being in line with your preference of having higher damage combos for being closer to the opponent. 3 damage and a knockdown seems like a lot if you're still thinking 1 hit = 1 damage, but if you were to do jump-in j.B or were able to start a close range combo with an A move, you would be getting much more damage than 2B.
Example Tenchi combos that are doable in the current game:
5A > 5A > 5B > 3B = 4 hits, 6 damage with knockdown and 1 unit meter build
With j.B jump-in, it's 5 hits, 8 damage
With min range j.A, it's 5 hits, 7 damage
With max range j.A, it's 3 hits, 5 damage (having to skip 5A > 5A due to range)
With max range 5B, it's 2 hits, 4 damage
And 2B alone is 3 damage
These combos would also do more damage if 2A was able to cancel into B moves further rewarding damage for being up close.
To look at it another way: If a person is really good at landing mid to long range moves on the other person and doesn't combo that much, doing so should be able to KO the other person faster than if he were to do that with a Light that does 1 damage because he is giving the other person many more chances to play.
As you can see from the numbers, this also helps normalize damage giving you an idea of where to set health and allow players the right amount of minimum chances per round. Currently, any combo starting with 5A will net you at least 4 damage, which ends the round in 3 bread 'n butter combos or 2 jump-in full combos with some stray hits/chip, or 2 half life combos (Naomi). Requiring so few touches makes the game more random because it can end super early or end in time up and is one of the reasons why one would naturally increase the default amount of rounds per game because more rounds gives more chances in a game where rounds end super fast or with very few touches (see Ultimate Marvel vs Capcom 3).
I think for Pocket Rumble, the combo damage I recommend you use to balance health is a max damage combo from a jump in j.B using no meter. Considering the combo examples above, and using the same damage values, I would start health at 30 to allow 3 full combos and 1 short combo and/or some chip to win the round. Meter spending will require less combos to win, but since you are using a resource, it makes sense to allow that. Then, health/damage can be tweaked accordingly (it is still alpha after all).
Point 2: Jumps beating lows
I think the fact that you can't punish someone for being in the air as hard as someone on the ground already makes jumping really good and does not need to be invulnerable to lows. When you get hit in the air, you get sent backward and are invincible until you land. The only way to get a combo on an airborne opponent is if all moves used in the combo cause knockdown. Tenchi's 4 hit combo with Anti-Air Antlers is a corner-only combo, otherwise you get 2 damage max. Naomi gets 3 damage from 2B > 2B > 1A and that's it. Along with the low damage potential vs airborne opponents, if you didn't end it in a knockdown, it essentially resets the game back to neutral potentially losing whatever positional advantage you had or might have had. In fact, if Tenchi hits someone out of the air with a non-knockdown move, he is actually
minus for trying to dash in for a mixup. He would instead need to be very close when hitting the button, then walk in to be able to pressure the opponent. You wouldn't use his normals as an AA anyway, but it's just an example of how jumps aren't terribly dangerous.
The other argument you brought up was that lows can be used to poke safely and still counter jumps on reaction. The problem is, so can the other moves. If I know you're going to jump, and I can't hit you low if you're jumping, why would I use a low to begin with? I would just use my anti-air move and get my 2-4 damage into knockdown/reset. If I don't know you're going to jump, I can also easily use 5A or 5B and would still be able to use my Anti-Air special to counter your jump-in if my 5A or 5B didn't already catch you. The only way Tenchi would get punished for using 5B to catch a jump is if he did it noticeably late. In neutral, you'd just go right into AA Antlers because he has no other good AA moves other than his 2 back specials, and on oki, you'd time it with the option select and can block or AA Antlers on reaction.
Jumps as they are now are actually very good and are not as situational as you think. Jumping is actually the go-to option if you think they'll go low at mid-range neutral forcing people to use mids to catch jumps and essentially negating the usefulness of lows. Tenchi can't poke with 2B if jumps can never be hit by it because he will just get punished for free for even trying it. Instead he'd be more focused on doing AA Antlers and 5B to catch jumps. If, however, lows were able to hit jumps, they would then be more situational due to more things being able to beat it and would require smarter use of jumps while still being good due to not being able to be punished very hard for being in the air.
Also, with variable damage, the times you're able to get a full Anti-Air combo would also be similar to grounded full combos further normalizing damage and making it easier to set a health value that will give people a good amount of minimum chances to play.
Point 3: Canceling 2A into B moves
It'd make 2A more useful as a combo starter because you would be able to do more hits and have an easier time confirming into something. It wouldn't help vs jumping if jumps stay immune to lows, but it would at least add damage to close range combos.
It also gives the player a general rule that you can do A > B > Special/Super instead of only 5A > B > Special/Super
Point 4: Transparency
What if you did 50/50 or 60/40 or 80/20 transparency?
Surely there's some sort of transparency setting that works that will let you show the game properly on 30 fps video while still looking good in the game.
Point 5: Crossups
The main thing about the defender moving away from the attacker on crossup is that it punishes the attacker for trying to crossup by sacrificing position as well as potential damage. Yes, it's tricky, but that's why it's a mixup. Mixups are supposed to be tricky so that you can fool the player into opening up to your attacks. They're still just as blockable as any other mixup (except for that throw OS which I'll talk about later). Giving less reward for crossup will enable players not to have to think as much about taking the crossup, because they know the reward is less than a normal jump-in. In a game like Pocket Rumble, I think crossups deserve the incentive to actually use crossups as a mixup tool without having to sacrifice position and damage.
Point 6: Anchor Point
I'm not really talking about jump arc and more about trying to do moves low to the ground.
Many times, I'm trying to time a deep jump in to get the most out of the stun of that move and make it easier to confirm from, but my move ends up getting cancelled early due to the anchor point hitting the floor. The best example of this is Naomi's j.B. The hitbox on that move is really narrow vertically and has less stun than her j.A so it is generally difficult to combo from whether it's a crossup or a normal jump-in unless you get it to hit fairly deep. I can't really think of a situation where, if I wanted to hit the button to do a deep jump-in, I wouldn't want the move to come out and hit. I'd pretty much always want that deep jump-in to hit. The only reason why someone might not want the move to come out would be to do a fake jump-in to get them to block high and then go low or something, but I'm not sure if Pocket Rumble has that kind of leeway to give a character a slow startup j.B just for that when it could be made more useful for general purposes.
In other words, I would rather have the move itself touch the ground before having to land instead of simply landing once the character's anchor point touches the ground.
New Points: Throw OS and Stun
Some things I thought up while writing this.
1. Why did you put throw on B? It creates a really good OS that pretty much overshadows any kind of honest high/low/throw mixup and lowers required thinking for mindgames. The only way out of it is to either tech the throw or do a DP. The defender doesn't really have a way to completely turnover momentum, just reset it back to neutral.
2. Why is stun the same for block and hit? I didn't research this much, but I remember a couple times where it'd be better balanced if certain moves had different frame advantage between hit and block.
Also, have you seen
Mike Z's video on FGs? I noticed a couple things he suggests that you don't do. One is the crossup thing, and another is trades. Pocket Rumble acts like the SF4 example (around 46 minutes in) and both characters immediately go into stun instead of showing their attack animations to make it clearer what happened. Just wondering how much of that video you might implement in PR.