I think you had to imagine that certain Transformers were bigger/smaller than others considering how whacky the scale of those toys were! I always imagined that Ironhide and Ratchet had heads, but behind their windscreens - much like War Within Ironhide and Kup! I would pretend that their windscreens had HUD (Heads-Up Display) that would allow them to do cool things like targetting and give them a live feed with up-to-date battle information. I also used to imagine that the S.T.A.R.S. base was a looooooooot bigger than they actually were. Typically it was just the main room of the Ark where Teletran-1 was... or like the bridge on the U.S.S. Enterprise.

You would have to imagine that the Transformers were more articulated than they actually were... like when they'd be walking, I'd just be making them "hop" up and down as they moved (like Muppets) but in my mind's eye they would be taking strides. Same with say a Battlecharger or Throttlebot using their hands/arms...

"Imagination is more important than knowledge." - Albert Einstein