You may note in one of my earlier posts that I pointed to 3 cards out of the Best Promos that would be likely to change the game: Professor Elm, Electabuzz, and Hitmonchan.
Professor Elm would be a good change, IMO -- only having Supporters for card-drawing is NOT a good thing. The trends for E-on do make Professor Elm's drawback a lot less powerful than it once was, but it is still noticeable.
Hitmonchan, though powerful, has one fatal flaw -- Psychic Weakness, which is exploited easily in E-on. Especially if it were ruled to play as the Best version (in other words, with 60 HP as opposed to 70), it would speed up the game, but not ruin it. Even without such a ruling, I am confident that E-on can easily handle Hitmonchan. Of course, it could limit play of Colorless types and Electric types, so it should be watched.
Electabuzz, as I mentioned before, could be a different story. It could make Water difficult to play. It may only do a maximum of 40 damage, but it does it for 2 Energy, namely (L)(C). And with Electric Resistance being relatively rare, Electabuzz would have little to worry about. Don't get me wrong -- I have long liked the card, but I think it may be too powerful to allow in E-on. However, it can easily be banned separately from the other Best Promos.
Honorable mentions go to Rocket's Hitmonchan and Rocket's Mewtwo. Those cards, in addition to Elm, I would play in some E-on decks, given the chance. Rocket's Hitmonchan is not as powerful as its Base set brother, but it can (pardon the pun) pack quite a punch. Its second attack is nearly as powerful as Hitmonchan ex's (lacking only the no-Resistance advantage), and its first attack is useful, too. With only 60 HP, it's not going to be especially hard to counter.
Rocket's Mewtwo would give Psychic decks, which are already quite powerful, yet another powerful contender. One of very few cards ever made with 3 attacks, it's a very powerful card if used right. Many of the strategies that could break it are not E-on legal, such as Focus Band. I think more than a few players would seriously consider it for slots otherwise devoted to Mewtwo ex.
Of course, I still don't know whether Nintendo was even thinking along lines similar to these, let alone the same ones. As I said earlier, I would greatly appreciate some insight as to how the fate of the Best Promos was decided. Given the chance to examine their reasoning, I could then help in the attempt to convince Nintendo to change their minds about this decision, or perhaps decide to lay the matter to rest. The latter is less likely, though.