[COLLAPSE=Regarding Wario Bite]The only example you posted that didn't still rely on a fortuitous occurrence of having a discreet hitbox or grabbox active during the end of the load time is the Wario bite. All others required timing and, essentially, a measure of luck. Why should Wario get that sort of exception? It's a pretty powerful one at that, since bite is a good starter for a number of Wario's strings and punishment options. So the Z/S player is doubly boned against a Wario, because they're now hamstrung by a telegraphed startup animation and indiscreet invincibility period which the Wario can abuse to take away the only advantage they were given in the whole affair, a free escape, because he can just hang a grab out there where they can't do anything about it, and then he gets a free bite to do with the Zelda as he chooses.[/COLLAPSE]
OK, so it's a disadvantage in one matchup. (Note that amusingly, it's actually possible for the transform to outlast the bite and Wario can be punished). Matchup-specific BS happens all the time, and this isn't even game-breaking. I don't see how it should be used to determine the merit of the entire mechanic. Also, the best case scenario is the same as that of the current system―you space the Transform outside of Bite range, no loading interruptions occur, and you can interrupt before he can bite you. Furthermore, the interrupt still forces Wario to use Bite, which may set up for some combos, but isn't the same as a fully charged Fsmash or meaty Waft.
[COLLAPSE=Regarding System-Dependent Load Time]Add to that the fact that with some players using their own textures in an effort to combat the load time problem, you get inconsistency across multiple setups in a tournament environment. While I'm also of the opinion that TOs should be disallowing custom textures to be used on tournament setups, this provides a standard of uniformity outside of the construct of the game itself. You can rely on the transform to have X amount of startup, Y amount of punishable cooldown, and a predictably consistent middle period whether you're playing on this Wii or that. All Brawl+ setups have Zelda textures, all Brawl+ setups have the same measure of control on the duration of the transform invincibility period.[/COLLAPSE]
But not complete control. SD cards, too, have variable load speeds, which are also dependent on whether you're running custom music or not (which often boils down to randomness when you have a mixed set of custom and default music). So, if you have custom content, the textures speed up the process and the music slows it down, and if not, vice versa. The point is, it's still quite variable. In any case, the modified mechanic doesn't assume any level of consistency (except in the case of grabs, which can't be shielded). The default mechanic gives your opponent an additional and randomized amount of time to reach you and punish you with anything they like. With the modified mechanic, they can only meaty you with a grab, and if they miss, you can punish easily, whereas you would not have time to with the default mechanic.
As far as the issue being with the transform being "unpunishable when used correctly," is there a move that
isn't like that and not regarded as crap? Why should you be punished for using a move correctly?
Specifically, I agree with Frag in that the momentum loss required to get off a transform is a sufficient price to balance the unpunishability. With equalized lag (in the beginning and end) you have more opportunities to get the transform off, perhaps, but you'll often end up eating a hit which, depending on percentage and stage position, can lead to an entire stock.