So I know there's been images and stuff out there for a few days on what the next pixelmon update is gonna look like. From the looks of it they're gonna be making Boss Pokemon more noticeable (they'll be noticeably larger and be tinted to match the color of their names). In addition it looks like they're working on having Poké-Centers randomly generate in various biomes, with each Poké-Center having it's own unique look based on what biome it spawns in. Honestly I really like the whole Poké-Center idea because it would save people the hassle of having to spend most of their first hour with the mod looking for the ores and resources to make Healing Machines and PC's.
As for the Boss Pokémon, I do like the idea of making them more noticeable, but I'm not sure about the idea of tinting them. Honestly the tinting would probably make them stand out a bit too much in my opinion, so they might need to lower the spawn rate a bit more to counter the fact that they'll be more easily spotted. I think making them much larger than usual makes enough of a difference visually without the tinting. Besides, it might make some people mistake them for shiny pokemon at first. It's not a huge deal either way since it doesn't bother me that much but it's something I'm sure they'll be taking into consideration before releasing the next update (which will probably be in Minecraft 1.6 since that update came out yesterday).