That's fine and dandy but check the second paragraph of that again. We'll still get this problem even if we use levels as a mere guideline.

"In this RP's case, we have a lot of options for paths we can take around the region, so there also comes the issue of... We may run into Pokemon way too powerful for us, we'll never be able to have a well-leveled team because if we all set them low so that encountering Pokemon too strong doesn't happen, when we get new members to the party they'll be underleveled."

Also if they become progressively harder then it just becomes a lategame mess. We lose variety, we no longer have a feeling of 'Pokemon in the wild', it becomes Dark Souls, imagine coming across a Magikarp that sweeps your party at end game? Yeah. A wild one too.