Certain evolution lines-I don't mind the odd ones like Numemon>Monzaemon or Patamon>Angemon but certain Digimon seem like they should only evolve from specific Digimon. For example it doesn't make much sense, to me at least, for Metalgreymon to evolve from anything but Greymon.
Rebirth-Especially in Adventure and Frontier its hard to care about death when they'll just come back. Like I think they should have kept death and just say Angemon "almost" died and used the last of his strength to start life over from the beginning and have Ken's crest of kindness brings Wormmon back (so it actually has a fracking purpose)
The fact that there's more Ultimates than Perfects. To me Ultimate should be like a legendary stage not something with more frequency than the level that is suppose to be a Digimon that has reached its potential. Same reason I dislike Super Ultimate. Ultimate is already "Going beyond the possible."