I don't like the idea of removing choices and options, but my logic here is threefold:
1. The use of Speed Thunder is a specialized skill. It requires a seperate skill when compared to using normal Thunder, and must be trained seperately. Those more skilled with using Speed Thunder will have an advantage over those who do not. Even then, only in matches with customs allowed. The use of Speed Thunder specifically against ROBIN is also a seperate and more specialized skill, though not to the same degree as using Speed Thunder in general, the ability to know when to use it against Robin specifcally is an additional skill that must be practiced in order to compete at the highest levels of a customs-allowed, Robin-only environment.
2. It represents an additional barrier to entry, to a tournament where I can tell players are already uncomfortable with participating if they do not feel they are strong enough. I believe we could agree that a Robin using Speed Thunder in a Robin ditto has an advantage over one that does not. I'm not saying that it is a better move, but in this situation, the advantages it grants (interrupting the opponent's Thunder Tome charging, for example, with your own sped-up "Thunder") make it basically a REQUIREMENT when fighting in a customs-allowed, Robin-only environment. When facing a casual Robin player, rather than a more fanatical Robin user/main who has practiced using her customs, the casual Robin player is at a disadvantage. I believe we should allow those with strong fundamentals, even if they're not a Robin specialist, to have a shot at competing in the Symphony of Scales. Of course, the Robin specialist will obviously have other advantages, but I do not believe they need to be accentuated any further than they already are.
3. Legitimacy. Sure we sometimes use some funky stages, but the tournament is otherwise legitimate. 3 stock, 8 minutes, no items. The strategies, combos, and techniques you have learned (with the new Arcthunder, for example) should work the same way they would work in a real tournament. Someone who has fought other Robins in tournaments, even if they main another character, should expect to be able to use the same defensive skills they learned fighting Robin in a legitimate scenario. They shouldn't be expected to adapt and learn new defensive skills and timings on-the-fly. And someone who has practiced their Arcthunder combos extensively shouldn't be expected to throw that training away because the work they have done is now somewhat overruled by the quickness of a custom move they never before had to or were interested in using.
4. Speed Thunder was the only custom move used. At least by anyone that made it in the top 8. (Not that all players in the top 8 used it, but I believe most of the top placers used it, including the #1 tournament champion) Me allowing the move would be more like "SPEED THUNDER ON" instead of "CUSTOMS ON". The original intention of the custom moves were to add some variety. Not to force anyone's hand.
Sorry if the points got a little blended together, but they do all relate to one another.
If Custom Moves become popular at large in the Smash 4 professional tournament scene I would consider revising the ruling.