I guess we live in pretty good times, there's not too much I can think off, but of course there's always things...
The Red/gold repaint and head remold of RID Megatron as Beast Wars Megatron. This was around a while back for a Botcon exclusive. I loved the colouring and would love to get my hands on this if it was ever made.
Masterpiece Galvatron - my favourite G1 character done up proper. This would NOT be Masterpiece Megatron painted purple.

Not sure if they would do this with a non-real alt mode.
Classics Predaking - I doubt they'd do it, but it would be cool if they were all voyager size so when they combined it would still dwarf all other combiners.
Masterpiece Rodimus Prime - Galvatron needs a nemesis... Again a non-real alt mode.
Masterpiece Cheetor - I wouldn't mind seeing them experiment with a Beastwars masterpiece character. I think other than Primes and Megatrons, Cheetor is the must done character, so he might be worth a try. Probably either his original mode or his Transmetal form. Again a non-standard alt mode, so who knows... It might be easier to work with the Transmetal one. BTW, this would look nothing like Supreme Cheetor form Beast Machines. I wonder, though, how much they could improve over the transmetal deluxe. You would think a lot, but really the deluxe is pretty accurate to the show. If it turned out well they could always do TM Megatron, TM Primal, Rampage, and Depthcharge. I don't really think this would sell well enough to do, but I wouldn't mind seeing it.
Movie Bruticus - Well, I decided to put something for the movie and I'd probably most want Bruticus. Devestator is cool and classic, but if I was a warrior robot race I'd make millitary vehicles that combine.
As much as I like Shockwave and Soundwave, I don't really see them being Masterpieces because of their alt modes. Cassette players are just old and a laser gun isn't going to look "real" which is part of what they go for. Maybe a Soundwave alt to go with the Shockblast alt...