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I think everyone agrees upon Rock Tunnel. XP
Besides that, I'd say the only thing I think the game could've improved on was the general flow. There are many moments where the player has to guess where to go and what to do, and many times younger children get stuck. (This is why I think most...
I will never forget my childish stupidity of erasing both of my Gold version save files: one had my first Lv. 100, my Feraligatr (could go solo through the Elite Four); the other was the one with my shiney Hoothoot. I had no idea at this time how rare shinies really were and my lame reason for...
My first shiny encounter (besides the Red Gyarados) was a shiny Hoothoot which--with full pride, to this day--I can say I caught and evolved! ^-^ This was after I stopped watching the shows, so I had no idea about Ash's Noctowl until about a year after that game was erased...(I was an idiot...
I don't really see an issue there, for even if you've caught every single pokemon you still have around a box or so left (evidence based off Generation 4).
It really depends on how low the Capture Rate is. If it's not rare, I almost always stick to those I want to add to my team first. But once I beat the Elite Four, I'm on a rampage with my Lv. 100 that knows False Swipe. XD