There's also the option of using in game rules to balance things out.....so what you could do is pick through those choices you don't think are meaningful because there is an obvious "better choice" there, and implicitly link a feat to that weapon. Then when designing your encounters, just factor in then additional power level to your CR. Essentially it's like giving everyone a free feat at level 1 - DM adjust accordingly.
So for example, Shortsword and club always come with Defensive Duelist. Flail and Morning Star get Savage Attacker. Greatclub gets GWM. Light Crossbow gets Crossbow Expert.....stuff like that. Or pick parts of feats to apply as abilities. So Warhammer might always come with the Shove part of Shield Master....that sort of thing.
Just spitballing ideas - you'll need to redress the balance though...