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Disclaimer: I don't have RMXP+Essentials so I can't tell you anything about how to do it specifically with what you've got.
I would assume the gist of how you would script something like this is to convert your sprite to HSV or HSVA from RGB/RGBA (just search RGB to HSV, it's a common beginner...
Just make sure that you do proper verification in your scripts. Obviously you shouldn't set up your code such that if you get a request to modify a game variable, your code does it without checking if it's legal and authentic.
In a nutshell, you can probably do everything needed for Pokemon...
Yes, building a new engine will be difficult and time-consuming. Yes, it will probably not be popular with the average user at first because of the need for porting older games and learning the new API. Yes, there have been many attempts to create new engines that have sizzled out and failed...
It just so happens that I've been toying with the idea of tackling a large project like this for my own practice and experience. In any case, despite not having personally used Essentials, here's what I've envisioned such a starter kit might need to include/accomplish:
Engine/Language
I...