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I feel like there are three big problems with Hoen.
1. The path through the game is garbage. In the first 2 gens, players could open up the map and tackle things in different orders. This did lead to leveling problems in GSC, but Hoen took the wrong approach to fixing it. Now you are trapped in a linear progression that has all kinds of inconvenient loops and one-way jumps. It's so bad that they had to put in a boat ride to get you to and from the second gym, and in the remakes you rival warps you around the map at least twice to save backtracking. The second half of the game is spent surfing the same big, repetitive, empty expanses of ocean.
2. The HM system in Hoen SUCKS. God damn you need 3 different Water HMs, and if you want to visit anything north of Mauvile you have to keep fucking Rock Smash on your team. If you were trying to utilize the new berry system, then your ass is going to have to navigate the map constantly using moves like Rock Smash and Cut, which gimps your team.
3. The pokemon variety is pretty week this gen as well. RSE was the first release that didn't have all of the available pokemon included across the three games. You could not get things like Magmar, Electabuz, Lapras, etc. The variety of new pokemon slowed down dramatically after Mt. Pyre. There's almost no new pokemon lines to encounter after the midpoint of the story. It doesn't help that that's when you start surfing everywhere and most surf routes only have two possible encounters.
Hoen isn't completely terrible, I like most of the Gen 3 mons, this was the start of double battles, this is my favorite berry system, the optional dungeons like the Regi caves and New Mauville were good additions, it's just there's so much wasted potential due to poor region layout and pokemon selection.
