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I think my biggest thing with Gen 3 was timing and features. Such as:
-Day/Night looking different
-Access to older Pokemon (That was more or less timing and fixed with FRLG, but still crap)
-Access to easy breeding/ditto (Fixed in Emerald and FRLG)
-Lack of anything to do postgame (Fixed in Emerald).
-Font being terrible (Fixed again in Emerald)
-Music being more hit or miss.
-Visuals looking like crap (Semi-fixed in Emerald, but not perfectly. FRLG had a better art style).
-Pokemon were carbon copies of earlier Pokemon, mainly since you could not capture certain ones at that point. Waaaay too many useless Stage 1 Pokemon (Fixed in later generations, but there is still a lot of useless ones).
-Hoenn was kind of a crap region, too much surfing and the actual layout was meh.
Emerald did fix a lot of what I had a issue with, but had its own issues (Like a weak Elite Four with no level ups, added stuff was hit or miss). I think R/S has the advantage of XY having a strong backbone to actually make it pretty fucking awesome and fixing a lot of the issues I had.
