Well, the only difference really between the two is which legend you want to battle first. I like HG more personally because you get to fight Ho oh earlier and Ho oh has some pretty epic battle music. Lugia's battle theme is good too. But it comes down to which legend you prefer. Ultimately it comes down to which legend you prefer.
Also there's the usual version exclusives. If you go to the main site and go to the HGSS link, then there should be another link showing which pokemon are version exclusive.