Been thinking about this question, in it's presented context- what could Honda have done better at the time...
Dual Discs in front seem like a pretty logical progression, and I love them on my F2. I think, though, that what the front end could really use before adding more brake is some stiffening and reinforcement. A good fork brace, proper springs, and tapered steering bearings go a long way. Ideally thicker fork tubes and a dampener would be utilized.
Then good swingarm bushings and better shocks-
Would have been nice if they hard plated the whole fork tube, and used better chrome throughout. Maybe find a way to seal the fork ear from taking on water, or maybe better yet, find a better way to drain/vent it.
Overbuilt switches. Would be nice if the stock ignition switches could handle hotter coils, and more powerful lighting.
Adjustable foot controls/sport control kit-
Factory design on the frame should be equivalent to Gordon's frame kit.
Better head studs/nuts/gaskets. Oil leaks be damned.
More attention paid to engine finishing- better blending of intake tubes into head, better valve pockets, no shrouding.
More attention paid to inner clutch hub- should have the HM oiling mods done to it from the factory.
YMMV, of course.