You can use RMXP Essentials if you want a custom at every style, but I think using RM2K3 BS makes it different and unique from other "Custom" Pokémon fan games. It would also make it more interesting because there hasn't been much RM2K3 games out there. Found of 20 so far.
I have to disagree with you there. essentials is much easier to master rather than creating almost everything required to make it look somewhat like a Pokemon game. you don't need to script at all to get yourself a working pokemon game in RMXP with essentials. (other than editing a few text files, which I don't count as scripting.)
While its true that RM2K3 is rarely used in Pokemon fan-gaming, I don't think you can give that as an argument. Maybe it would be from a developer's point of view, but I doubt many people interested in playing a fan-game won't care.