I can understand all the frustration of the seemingly infinite # of skylines, Evo, WRX, RX-7 etc. and I agree that other cars (historically important or just for greater variety) could've been included, but please look at this issue with a bit more logic.
Living in Japan currently, I can tell you that I really do see many of these slightly different versions of the same car driving around. With GT's first market being Japan (regardless of how big the US market is), is it that hard to comprehend the fact that Japanese drivers might want their particular version included? Yes, KY is a GTR nut, and the game is mis-labeled as a "history of" for PR purposes, but I can tell you that of all the GT fans I've talked to here (and I've met quite a few) don't mind having less American/European cars if a special-colored limited edition skyline can be had in the game.
It all comes down to audience. Of course Americans/Europeans would complain about having too many skylines, etc (though I'm sure just as many are glad they have a chance to drive the versions of those cars that didn't make it to their country). In the same way, if more muscle cars or maybe all the trim levels of the Dodge Neon were in the game, the same complaints might be heard from the Japanese market. The only real way to fix this is to either have region-specific GT's or try to appease everyone by including more cars (possible with GT5?).
All that being said, the cars I personally could've lived without are the ones you can't use in actual races (Nike, old carriages).