Originally Posted by Skylands
HeartGold and SoulSilver differences just pertrains to certain Pokemon that are only available in one version, though there are some tiny
storyline differences too.
The exclusive Pokemon for HG are: Mankey, Primeape, Growlithe, Arcanine, Omanyte, Omastar, Spinarak, Ariados, Gligar, Mantine, Phanpy, Donphan, Sableye, Baltoy, Claydol, Latias, Kyogre, Mantyke, and Gliscor.
And in SS: Meowth, Persian, Vulpix, Ninetales, Kabuto, Kabutops, Ledyba, Ledian, Delibird, Skarmory, Teddiursa, Ursaring, Mawile, Gulpin, Swalot, Latios, and Groudon.
So it's up to for you to decide.