Ys and Last Remnant aren't even remotely close to Golden Sun. Frankly, there is pretty much nothing. Breath of Death VII, Cthulhu Saves the World, FF7 and FF8 are the only traditional JRPGish games I can think of offhand that are native to PC.
http://i.imgur.com/ULj4q.jpg Let strength be granted, so the world might be mended.
Good sir, I implore you to join the PC+3DS Master Race. You get the best of both worlds. Want the best graphics, multiplayer, sales, and control scheme? Play on your PC. Get that JRPG/Mario itch? Whip out the 3DS.