I already have individual icons for each Pokémon. I do plan to color them by species instead of all red; however, an attempt to copy Prism's code directly failed, so I may end up designing my own.
Prism has an entire separate audio engine for playing its new cries, and I don't want to copy signature features like that. (Same goes for the compressed text engine, printing variable-width text, trainer appearance customization, the calendar, and so on.) If I manage to use the existing cry system to better approximate the official cries, that's something I can add in a later update without breaking saves.
There are a few smaller features of TPP Anniversary Crystal and/or Prism that I'd like to have: playing the "low HP" beep for just a few seconds, a sparkle animation for successful captures, a Surfing icon that has the player's head instead of always Lapras. But most of those are just because we both want to copy the new official games, which do all of those things. It might be easier to implement some of those myself than to adapt existing code.
(I thought Polished Crystal would be the first GSC hack with official abilities, thanks to FIQ's help, but then the TPP Prism playthrough disproved that. So congratulations to Koolboyman and company. It'll be interesting to compare our separate implementations. I think the Prism devs did more refactoring of the original pokecrystal code than FIQ and I have, at least in some parts.)
(Oh yeah, apparently there's a Haunted Mansion in Prism? Total coincidence, I'm adding one in Polished Crystal 3.0 based on an old idea by Mateo. :P I hope they don't end up too similar.)