I do think the OT rule is a brilliant idea to give newer, less wealthy trainers a fair chance at winning. I also, however, understand the frustration of the top tier of veterans who have shed blood, sweat, and tears gathering their pvp pokemon.
Perhaps the best option, as someone mentioned earlier, is to have two separate tournaments with slightly different rules. One being limited to OT pokemon, the other being an anything goes (OT or not).
Unfortunately, this would undeniably separate the skill level of the participants in the respective tournament. The most experienced pvp veterans would all be in the anything goes bracket, while the OT bracket would see mostly newer trainers and the occasional OT enthusiast veteran. So perhaps the OT bracket would be dominated by experienced pvp veterans who have invested a significant amount of time to catching and training their own pokemon.
It seems like there is no easy way to go about this, I just want you to know that all the staff's work is insanely appreciated. You can never please everyone, that's just politics.