You make some good points.
An uppercut isn't really the right word, it's just an upward claw slash, since he's basically just throwing his talons. It's really similar to your acid spheres, but those would look strange if they were to move slowly in the air, while a slow Razor leaf-like projectile makes a bit more sense to me. I'd use the acid as an upSmash instead.
The shoulder bash is more about the utility of the move rather than being canon, but yeah, lack of source material is gonna be a huge problem, since Kraid has even less appearances than Ridley. We'll have to take creative liberties at some point.
I'm pretty sure that NeutralB can be made, I'm far from being a PSA wizard, but i know enough to say that the following can be done: The model changing according to a variable (Pit does it), moves changing according to a variable (Samus' Fire/Ice beam), and a move charging on it's own (Wario's downB, ROB's neutralB; Having NeutralB charging by itself might actually be a bad design choice when you think about it, so maybe it's not even necessary).
The way i see it, when you use neutralB you shoot the 3 spikes at once. Now that you mention it, i didn't not think of the implications of each spike being a separate projectile, so instead, it works as such: all 3 spikes are shot at the same time, traveling for about 3/4 the lenght of FD, maybe a bit less, and those 3 spikes actually count as one projectile going straight forward (So it really similar to samus' charge shot, maybe a bit slower and with a different damage/knockback ratio). The point is, as long as you hold the charge you force your opponent to approach since they can't reliably camp, and that charge can be used to punish anything stupid you opponent could do out of your physical range. It does sound strong, but PM!Wario's sideB is just as strong: what i mean is, there are counterplays, just get through Kraid's wall of hitbox and pressure him, and he won't have time to shoot; Or bait this move, and Kraid ends up without his strongest projectile, his disjoints, and he'll have to get vulnerable to get them back (this why i say an autocharge may be bad, since Kraid just have to wait and he'll get back that advantage you just forced him to drop).
I have no doubt Frayark will deliver quality content, but what i mean is his proportion don't really fit a fitting game like smash were even the slowest of characters have to move around: his legs are too short for him to jump or run, and his arms don't really allow any clawing moves. It's a great design for the fortress-like boss he is in metroid, but it doesn't really fit smash sa much as the melee model, which has longer legs and arms, a proportionally shorter body and more mobile head.
I agree, though i think we should postpone it untill developement actually starts.