I would have liked to have seen the Mitsubishi Lancer Evo VII rally car, both the prototype (from GT3) and the actual competition car (from GT Concept) return. Why they never returned after those games is beyond me, especially since the bug-eye Impreza managed to keep both its prototype and finished model all the way through to GT6. Even weirder that they brought back the Korean-exclusive Hyundais from GT4 (Click Type-R for example), yet not these.
Other examples are the Toyota GT-One road car, which with a bit of fixing up could have been a very good standard from GT3 (the body is fairly simple). As others have said, the Toyota Motor Triathlon Race Car and the Nike One from GT4 would have been interesting; the latter in particular as the GT Vision concept appears to be named the Nike Two, so it could of had its predecessor in there. The Toyota pod from GT Concept would have been a laugh too.
As an extra, it could have been cool if they added in the deleted cars from GT Concept; some of the more basic ones reappeared in GT4 anyway (like the Fiat Barchetta), but the more unique variants like the RAZO Edition Fairlady Z concept, and the Mini Cooper S rally car thing.
If Porsche appears as a DLC pack, I can guarantee the 911 GT3 deleted from, er... GT3 will slide in there as well.