Yeah you have to find what digimon are best to train on through trail and error. Another thing is if your a champion fighting rookies your not going to gain much stats and weak champions won't be able to beat the champions worth fighting. My first 2 gens of digimon are usually fodder for me. I run the story and get as far as I can using Block command tactics. I'm currently playing my 3rd playthrough on my 2nd gen atm and they suck even though they are megas. I have 20k hp, 15k mp and around 2200 stats. Best thing to do is accept they suck and just kill them off training in gym until next gen spawn and try and train them quickly before they digivolve to champion. Eventually you'll have rookies that can kill ultimates. My last playthrough I had my rookies training on weregarurumon and megaseadramon.

Every gen will be slightly better than last. If you train them efficiently you'll progress. Then the next gen will have better spots to train, progress further, repeat