The gameplay has improved drastically since the GBC versions, and looking back on it now, the first generation of games were absolutely terrible to the point where replaying them is painful. Your best bet would be to get either Heartgold/Soulsilver or Black/White, since those are the two most recent and they've arguably the best gameplay. Black 2 and White 2 will be released in a few months as well.
Don't listen to people who say "anything after the first generation is shit" because that's simply not true.