Same for me, there's really only 2 exclusives in each game that I care about. HG has Kyogre and Claydol, and SS has Meowth and Skarmory.
Heart Gold's exclusives are technically better. In gen 3 Claydol was the best contest pokémon and Kyogre was the strongest in battle. I don't know much about gen 4 pokémon though; I haven't played those games.