>>57033211pixelmon is mostly just developed for the legions of officially affiliated copy and paste p2w servers, and also as of recent years it's been bugging out due to shitcode to the point where battling (you know the only real multiplayer activity to do in pixelmon) regularly seizes up and softlocks due to desyncs, which is obviously a very bad thing
i don't think it's been fixed
also performance reasons; pixelmon models are very badly optimized (and glaringly out of place in a block game, too) so having more than a few dozen on your screen would cause lag if you don't have a high end computer
additionally, pixelmon's focus seems to just be gluing on pokemon battles to minecraft while disabling/gutting major features, whereas cobblemon seeks to integrate itself with vanilla and actually compliment both vanilla and other mods
also cobblemon model animations are much more kino and animated, whereas in pixelmon they mostly just breathe idly or have a walking animation not in sync with their actual movement speed so it looks like they're skating on ice all the time