I completely forgot Super Rod Pokémon and fossils once you get to the Underground. But I put everything into one convenient Pastebin detailing all 493 Pokémon.
http://pastebin.com/nbYSzbXKtl;dr
>Ruby and SapphireSingle-player only (no trading or events, use Ruby OR Sapphire)
Hoenn Pokédex - 180/202 (89.11%)
National Pokédex - 180/386 (46.63%)
Multiplayer assistance (trading between Ruby and Sapphire, non-distribution events)
Hoenn Pokédex - 200/202 (99.01%)
National Pokédex - 200/386 (51.81%)
>Diamond and PearlSingle-player only (no trading, Pal Park, Wi-Fi, events, or dual-slot mode, use Diamond OR Pearl)
Sinnoh Pokédex - 132/151 (87.42%)
National Pokédex - 357/493 (72.41%)
Multiplayer assistance (trading between Diamond and Pearl, dual-slot mode, non-distribution events, but no Pal Park)
Sinnoh Pokédex - 151/151 (100%)
National Pokédex - 441/493 (89.45%)
So yes, while Ruby and Sapphire have a roughly 33% larger regional Pokédex, Diamond and Pearl have far more Pokémon availability overall, as well as a much larger post-game.