I think it depends on the kind of game that you want to make. If you want to make something that looks and feels the same as the official Pokemon games, Pokemon Essentials does that the best. If you wanted to perfectly recreate a Pokemon game, for example, I think that would be hard with Crystal Engine, but really easy with Pokemon Essentials. Or if you just want to add a new type and make your game around that, Pokemon Essentials is definitely the way to go.
But if you want to tweak some stuff, then using VX Ace might be easier. If you want to remove the 4 move limit, or make a crafting system, or just... anything that a normal Pokemon game just does not have, then VX Ace probably already has a script for it and you can plug it in. You can mix and match scripts and features.
So, VX Ace and the Crystal Engine are definitely worth using, (and it's free to download the Crystal Engine so there's no harm in playing with it if you already have VX Ace) but it's better suited for... more non-traditional Pokemon fangames, I'd say.