I think 2 on 2 was fine for all the early matches. Many Gym battles and some of the early league battles (like the first rounds in the Hoenn league if I remember right) were only 2 on 2. The semi-finals in Alola were 2 on 2 as well. Overall the number of pokemon used isn't really an issue, for example Candice's Gym in DP was a 4 on 4 and a lot of it was kinda rushed so it didn't matter. 3 on 3 or more doesn't make it feel any more or less important.The difference is that those two-on-two League matches were usually qualifying rounds for the actual tournament. Then it was three-on-three matches and then full battles for the later rounds of the League. There's no consistency like that with the PWC. Even in the Hyper Class, we still got a one-on-one battles. Going back and forth on what format they wanted to use for each match just made it feel like a mess.
I'm not saying that two-on-two battles are automatically bad. Ash vs. Korrina was the first PWC match that I actually enjoyed and I thought that the first two Bea matches were pretty solid too. Ash vs. Iris wasn't bad, but I do think it was a bit too rushed and probably would have been more enjoyable as a three-on-three match instead. As much as I hate the one shot character matches, I did like the battles Sirfetch'd had prior to its evolution too. My main problem is that winning a one-on-one match and arguably two-on-two matches as well just doesn't come off as particularly impressive. It's really hard to make defeating one or two Pokemon feel like a huge accomplishment. And considering the the bulk of the PWC was built on these kind of matches, that's a problem. Defeating three Pokemon or half of a full team is generally more effective. It gives both side a chance to potentially show off their skills, give their Pokemon more chances to shine and can make the victory feel more impressive/earned.
Obviously, none of that is guaranteed either. There are plenty of bad battles throughout the anime's run even if they are three-on-three. I just think that kind of format is more ideal and would have helped to make Ash climbing the ranks to the Master Class feel more impressive, as well as making the PWC feel like living up to the hype fans created for it.