Donkey Kong was never a real popular character, and Nintendo themselfs are to blame for backstabbing Rare and create **** as Jungle Beat and Mario VS Donkey Kong (PAON is doing a great job on DK games though but noone cares). And even at DK's peak of populairity (the Rare era) Diddy and probably even Dixie quickly grew more popular than him cause they where both playable twice.
His 'slowness' (even though he's like.. the fastest heavy weight in Smash) clumsyness, not too many reliable moves and lack of real flashy moves in the Smash games also doesn't help his popularity either, cause most people will prefer the faster characters making people who even DO like DK not wanting to play as him.
The way I see it, is that Diddy is just more popular than DK and easier for people to like in Smash through his quick moves and other features which makes him *sign* better than DK. Sure, I love Diddy and everything (lol my username says everything) but even though I was a DK main in Melee and secundary in 64, I so far can't bear playing as DK...