I haven't played the game yet. Not sure if I will. But I've seen some gameplay, and, honestly, it bothers me too, and not just because beating up Pokemon feels bad. My main problem is that it could have been done in a better way that would make me feel less bad lol

The pals should be dangerous! Even the basic starter ones!

I play a Pokemon TTRPG where you can beat up Pokemon with your bare hands if you want. The difference is, they're not helpless. A trainer without any investment in their personal combat skills is roughly a suitable match for a low level Ratata. Even in the video games, there's a reason Professor Birch got cornered by a couple Zigzagoon. It's the same reason you're not allowed in the long grass without a Pokemon.

Pokemon are magical monsters that can just straight up kill you. There's a big difference between fighting something like that, on basically equal footing, and punching a helpless stuffed animal.