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As has been mentioned already, there was the overhaul of the IV/EV's compared to Gens I and II, including gender not being based upon this anymore. Abilities were also added in Gen III which further made another layer of incompatible data that would have needed to be randomly generated with no prior code existing.
From a bit of an older player's standpoint, this really did hurt some of the player base continuing with Pokemon including myself at the time. After playing through Sapphire and being unable to keep my Gen I and II pals alive I felt somewhat upset that it had to be that way. This led to me "growing out" of playing Pokemon, at least on a system (roms allowed me to play gens 4 and 5), until I decided to buy a copy of X and a 3ds a few months ago. Put aside the 'genwunner' type talk because Pokemon is just as fun as it ever was, if not more, but it will always leave a bit of a sour taste in my mouth (even though I understand why Gen II isn't compatible with Gen III).