Yeah, I really think the Gym system hurts Pokemon in the way it's set up right now.
The idea of "beat the 8 gym leaders to challenge the League" isn't a bad idea in itself, but it is starting to get a little dated. It's standard and boring enough that I bought Black 2 and NEVER FINISHED IT. I didn't even get all 8 badges-I just stopped playing when I beat Skyla and took her plane to the other side of Unova, and then I was like,"time to explore another boring town, do another boring cave, and then fight another gym". Honestly, it should never feel like that. While Hoenn was BY FAR the most HM-dependant region, that felt fun because you would run up into some area you couldn't get through, and then you were like,"I can't get through here, I need to come back later." Even after Fortree it wasn't so linear that it was boring-sure, you had to do certain events in a specific order, but once you cleared out the Magma hideout you were free to explore. Want to go check out that random city dot at the bottom of the map? Go ahead, stock up on healing items and check it out! Want to head to Ever Grande City? It's blocked by a waterfall, I need to figure out a way to get up waterfalls! That kind of gameplay is healthy and fun.
As for the storyline, both Mystery Dungeon games BLOW THE MAIN SERIES AWAY in terms of storyline. Yes, the gyms are a crutch which allow Game Freak to push out near-yearly entries...but soon Game Freak is going to have to make a choice between Pokemon being a yearly cash cow or Pokemon being an evocative RPG experience like Skyrim or Tales. Mystery Dungeon is more on par with those-sure, it's a side game that isn't part of the main Pokemon canon, but the story in Explorers of Time/Darkness/Sky is extremely well presented and told WITHOUT being tied to a linear format like the main pokemon series. Sure, there was an order of dungeons to go through...but it wasn't just "I reached the next town, time to do a gym!" You could go do other dungeons, you could do side missions, and every time it was new and unique.
Mystery Dungeon holds the distinction of being the only pokemon game where you can get a truly different experience on every playthrough, kind of like you can in Borderlands, Skyrim, and other RPGs and RPG/fill in genre here hybrids. If anything, the main Pokemon series should be more like PMD.