For whatever reason EZ-Flash decided to name the extension of all Emulator SaVes .esv. This kernel includes a bunch of plugins for a lot of systems using the various emulators (smsadvance, cologne, pceadvance, etc) as separate plugins but didn't extract the pocketnes/goomba color emulators from the kernel (sort of a needlessly tedious thing without any real benefit) so saves are compatible with them.
If you want, you can override any extension (even gba) with whatever plugin you have. Anyways, that won't help because apparently Goomba Color isn't compatible with Pokemon Crystal and Pokemon Crystal requires Gameboy Color support. You're, of course, free to take the Goomba Color source and try to fix it, but AFAIK no one (beyond maybe Dwedit) has bothered trying. I do know it probably wouldn't be easy, presuming it's doable to get it running at all at a decent speed. Gameboy Color really is beyond the limits of what a Gameboy Advance can do*, which still rather impresses me.
* In much the same way doing XBox on XBox 360 isn't really doable. Ie, given enough time presumably you can make a variety of games work with a lot of specific optimization, but getting even 80% compatibility with lots of glitches doesn't seem likely unless you're willing to devote tons and tons of time into it. :/