I would list:

 

[G1 Optimus Prime]

G1 Optimus Prime

G2 Optimus Prime(with sound pack)

Black Convoy

New Year's Convoy(with Necklace?)

Convoy(2003 reissue with Energon Axe)

Limited Gold Convoy

(UltraMagus(white convoy)

Ultra Magnus(Matrix Glow)

Ultra Magnus(movie Preview)

We don't complain much about this issue because besides the Gold, Black, and Ultra Magnus versions, they are all basically the same colors

 

(And you forgot Hasbro Reissue Prime)

I'll complain about the Hasbro Reissue Prime for having short stacks. Hasbro reissue of Powermaster Prime is really nice though, since it takes after God Ginrai.

 

What I have notices is that people don't normally complain about the G1 repaints and remolds. Sideswipe and Red alert are repaints of each other, likewise with Prowl/Bluestreak.

 

I personally have no complains about Binaltech Streak as a remold of Binaltech Smokescreen.

universe repaints of bm drone into skywarp and bw tigerhawk into razorclaw

I'll say that the universe R.I.D. magnus and prime were the best.

Black Zarak

E-Tidal Wave

Armada Predacon

Botcon Cyclonus

Alt Dead End

RobotMasters G1 Starscream :tfevil

No-one seems to Starscream much about Skywarp. Come to think of it, no-one mentions the Armada seekers much, despite the fact that they had probably the single best modes to come out of it.

tfu sunstreaker and sideswipe

id say rid scourge. the excellent repaint made a unattractive looking g2 prime into a menacing evil twin!