Small guys might not draw, but I don't choose my entertainment based on what attracts the biggest part of the masses. I look for quality and the best wrestlers in history, as far as my tastes go, have been smaller guys. Jericho, Guerrero, Benoit, Punk etc are people I'd always pick over the big roid monkeys. Of course there has been a few big men that's been really good as well. I was always interested in seeing Lesnar in the ring, but Nash was definitely never one of those.
Boxing/MMA comparisons don't work when it comes to a 'fake' TV show. With boxers and MMA fighters everybody knows they are fighting in a legitimate competitive event. There is no suspension of disbelief because it's real. In WWE, that isn't the case and they aren't the same thing. The vast majority of casual fans are tuning in to see the guys they won't normally see on the street everyday. That's why Daniel Bryan could never do or be to them what John Cena is to them. It doesn't work that way. I hate to drag this up but just look at the problems Punk is having and he isn't even that small. Getting people to buy into you as a main event star is one thing. Getting them to buy into you as THE main even star is something different entirely. You need to have the physical presence to pull it off which is once again why guys like Cena play the leading man role and guys like Bryan play as a member of the supporting cast.
While I agree to a point I don't think it's as drastic of a difference as you put it. In boxing/MMA you still have the lingering aspect that the smaller guys can't beat the HW's, so the best fighter in practical terms is the best HW. What the weight classes show, however, is that there are other ways of defining what "the best" is. It can, for example, be the guy with the best technique, which you won't find in the HW division.
Even in boxing/MMA you'll still generally get the less educated masses the most interested in the HW's, so the phenomenon is still there. Of course the biggest current draws are Mayweather Jr and GSP, in their respective sports, so it is possible to change that, and the same should be possible in wrestling. It would take some work to get there though, just as it took time before people started getting real interest in the lower weight classes in boxing when it began.