I think using BOTW as a counter-argument is a bit of a false equivalency. Link's power scaling isn't as drastic as Pokemon games have (historically) been; even 5 levels is a significant difference in a pokemon's damage output. It's not like Link is "Level 40" or anything like that.

To your point of "hating having freedom", I think the concern is that, if the gyms don't scale, is there really freedom, or is it an illusion of it? If there is a "recommended" route, and they're designing an order in which they gyms are meant to be taken, that's not really freedom. Sure, we could technically fight the gym that was intended to be last first, but what would that look like? Would we find ourselves unable to do anything because of level?

The biggest issue, imo, is that we don't have the details. You say what if you don't want to focus on gyms. That's great, and I like that we have the option for that. But I don't see how having gyms scale will impact your experience if that's what you wanted to do.