I am going with RF1 for just one reason. The numerous bugs the HMDS had. I really liked it but it sucks to play happily and after 5 season lose everything because the creators just published it to steal money from their fans. If it was not so full of glitches then I would not even compare them since Rune Factory and Harvest moon like the title suggest are 2 totally different game from a bunch of perspectives. So you better decide either if you want to play a harvesting gave that go around town talk to people marry and have fun with the little festivals that remained or go with a fighter to save a town and in the meanwhile try to get a bit friendly and have some crappy festivals to look for.
When Harvest Moon DS Cute comes out I bet I will pick that but right now I am picking Rune Factory 1 since it is out at least and a really good game. Even though it was a really close tie between that and Cute.
Why was Rune Factory 2 there, should have been Island or something.