While Crystal added a great storyline on the Beasts and Ho-Oh, I think it still falls in comparision with RBY. GSC Pokémon are nice, but the game isn't. And well, when I went back to Kanto, I though: "Damn, another 8 GYMs? What's the point?". You said it yourself, PKMN Master: the original feeling was lost with pathetic excuses. While I was OK with the loss of Cinnabar Island, as it seemed kinda reasonable, the other caves collapsing is totally pointless. Unless the Cinnabar eruption caused a MAJOR Earthquake in the whole Region that caused Mt. Moon, Rock Tunnel, Victory Road, Unknown Dungeon and Seafoam Islands to reduce dramatically in size, or collapse, it's totally pointless. Man, even Team Rocket butts in with the stupid Generator thing.
The Safari Zone closing is another stupid excuse for memory shortage. Man, they should've made Johto bigger and deeper instead of fitting a crappy Kanto in it... oh well. RS is HUGE and an awesome game in comparision with this sub-par generation. The Teams might be pointless in a way (Most people thinks that, I don't know why...), but they're more threatening, almost like the RBY Team Rocket. Come on, they ALMOST reached their vision of the perfect world, but couldn't control the wrath of the Mythical Pokémon. The plot is a bit deeper, and it's nice overall. Instead of the plains-forest-caves trend we had on RBYGSC, we now see Deserts, the deep ocean, a Volcano, falls, and overall more varying scenario. Everyone thinks differently, but I'm glad RS didn't have another friggin' Region. It's a pretty long game by itself, and having another useless trip just to beat the Legendary Trainer is a waste of time, as GSC was...