My 1992 wagon accord overheats when I'm doing highway speeds because the rpm's go so high , for some reason the automatic transmission is only 4 speed instead of 5 like a manual so when I'm going 65 it's all the way up to 3x rpm's. When I'm just doing town driving the rpm's never get that high so it's stays perfectly cool.

Is this like a design flaw or is it like broken in some way? I have a manual 1990 accord that is 5 speed and never overheats.

 

No, the auto transmission is supposed to be a four speed. Your car is not overheated from highway cruising. The cooling systems on those cars have enough capacity to run that high, more than enough. You need to look at your cooling system.