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Very small roster of shadow pokemon, most of your good options are pretty late game. Have to find a pc to save. Human models were hot garbage except for like 5 semi-decent ones and gen 1 and 2 pokemon reuse their stadium models. No routes, only towns and a few dungeons. No wild pokemon, no breeding, also means you can never get more pokemon than 50ish pokemon in your save file. The only controller less ergonomic than the gamecube's is the n64's and you're gonna be holding it a long while. Celebi and plenty of e-reader content locked to Japan. Battles can be really slow, grinding is a bitch. A lot of the music is just the same few pieces with slightly different arrangements and styles. There's some glitches that can occasionally prevent certain rematches from triggering so it's possible to get locked out of a pokemon, had this happen with remoraid on my 1st playthrough.
I'm sure I could go on, and the sequel fixed a good deal of the issues, but Colosseum is still an excellent game despite its flaws.