I've also been maining Necalli since the betas, and while I'm no fighting game pro, I don't think I'd agree with you here. I'll try to respond just based on what I've been seeing as someone who just reached Silver rank.
His crush counter game is fine, and just because he can't convert each one into a full combo isn't necessarily a negative since he has so many of them. His anti air crush counter is pretty useful, and can be followed up with a sweep if you're within range for decent damage. Plus, even if he's out of range, a crush counter will sometimes allow you to close the gap and get in, which is exactly what you want as a Necalli player. Like I said before, he's got around 5 different crush counter moves, so I'd say that the reason st. hk has so much pushback is because they probably wanted to make each one useful for different things. There's also nothing wrong with some random crush counters just for the raw damage, since the damage will add up with all his CC options.
Isn't Necalli one of the few characters who has 3 frame jabs? I've been getting a lot of milage out of them just by interrupting the opponent, and on counter hit you can get decent damage by going into cr. MP > special.
Necalli's normals are pretty good, so I don't think he's as bad at footsies as you're making him out to be. Knowing your range and throwing out his MP can get you a lot of hits/counter hits that can lead to combos. You can use the stomps to advance on the opponent, and while LK stomp is technically not safe (-4 on block) I think if you get the spacing right it's really hard to punish. MK and HK stomps are safe (-2 and 0 on block respectively), and I've found throwing in a MK stomp after a blocked cr. MK is a pretty good frame trap that can lead into a full BnB combo.
It's not great, but it's situational. If you've got them conditioned for a certain approach, sometimes a divekick can throw them off. It's also not terribly unsafe if you aim for the legs, as you should be doing.
V-Skill is great man, you just have to know when to use it. If someone wants to turtle from full screen, it gives Necalli an option to pressure. I've gotten a lot of mileage out of it at long distances, and on hit it gives you enough to time to get a few dashes in to close the gap. It's especially useful against Gief.
Bison is the frametrap/normal king, but I honestly don't consider him too similar to Necalli. They've got different playstyles, and I think Necalli exceeds in areas that Bison doesn't, like general rushdown, he's got more full screen pressure, etc.
Necalli doesn't have that more crush counters than most cast members. He has 4 (including sweep) (Necalli's cc are st.hp, cr.hp, st.hk, cr.hk), which is as much as the majority of the other cast members. Unlike the other cast members though, 2 of his crush counters lead the opponent to an aerial spin state that cannot be followed up on by the major tools in his kit. Compare this to Bison, who also has 4, except all 4 of his crush counters can be followed up on with a regular combo, or compare this to Ken, where two of his crush counters do put the opponent into a non-grounded state, but is actually perfect for Ken's kit, and you see how the aerial spin is specifically designed to not allow Necalli to get full damage off one of his best buttons/2 of his best crush counters (st.hp/cr.hp).
Necalli does have a 3 frame jab. It just has more recovery than most jabs, and it has less range than most jabs too. I've been throwing out cr.mk->mk stomp since beta 2- its been a fantastic frame trap, but once you start playing against higher level players, it does. not. work. Again, great tool against new players or starting players, but intermediate & experts see right through that stuff. Not to mention all the start up cr.mk has to go through to get its active frames out, in comparison to other cr.mk I mean. cr.mp is easily his most versatile normal, but its range isn't anything special, and to get a full conversion on a counter hit, you still need to be super close. ALSO, cr.mk does not give you enough block stun to negate the startup frames on mk.stomp. I have been ROUTINELY jabbed out of mk stomp after cr.mk by opponents who knew what they were doing. Its why I switched to cr.mk->lk stomp, because at least then I am guaranteed to get the chip damage on block and before potentially eating a jab.
The divekick is terrible. It's unsafe at any range. Compare the amount of startup it has in comparison to the other dive kicks in the game, even the ones that do not lead to anything (Rashid), and its easy to see just how terrible it actually is. Its very easily reactable. It's hitbox range is as short as his jumping hp, except you actually get more horizontal coverage with jumping hp. Even if you get a late-hit by nailing a toe, assuming your opponent didn't punish you hard, you're still too far away to get anything meaningful. You'll get a jab, and then the opponent is out of range except for ex.stomp.
Let's not mince words here - Bison pressure DESTROYS Necalli pressure. The reason for this is Bison is generally safe on almost all of his pokes & pressure tools. Pressing buttons on stuff you think should be punishable generally gets you blown up by Bison. And Bison has amazing tools at getting in that are more than just dashing forward. And on top of that, Bison's dash actually has invincibility frames, something that Necalli would thoroughly enjoy. Bison's v-skill & reflect are also far better tools at full-screen than anything Necalli has. Necalli's charge move doesn't even go full-screen unless he ate a fireball on the way there. Bison's aerial stomp is a far better tool at getting in, because at least it has mix-up options instead of being entirely predictable.
Necalli's v-skill would be infinitely better if the hit box on it were 2-3 pixels wider & higher than it is. As of right now, its entirely too easy to whiff things because of how tiny it is. Compare this to Viper's seismo in SF4, and you realize that its purpose as a tool is just too limited here in comparison from what it derived from.
Necalli's DP is just as laughable. No low-profile hitbox for Necalli's DP means you are going to whiff it way more compared to the other cast members. Go to the training room, put the cpu in the corner & set them to block, back away a little bit & do a necalli dp - you will clear their heads every single time. Compare this to the other DP's in the game, and you see how short changed it really is.