When it comes to the general public, I believe that most have some fond memories of playing Donkey Kong Junior as a kid. With Donkey Kong 3 it's, "They made a third Donkey Kong?"
So in the public I really believe that if they had to play a game they would play Donkey Kong Junior.
Having said that in the competitive world, it's a completely different story. It's not that Donkey Kong Junior played normally is a bad game, and if you do an hour time limit on Donkey Kong Junior it's not that bad.
But when going for high score, it drastically changes. Half the game is straight up point pressing, but unlike Donkey Kong the point pressing is mostly repetitive, and not challenging at all.
So half the game is doing the same action over, and over, and over, and over again. Personally it wasn't that much of a drag on me, and I was fine with it. Most gamers though are not like me, and it's becomes irritating for a lot of gamers to go for a super high score.
Now Donkey Kong 3 is a different beast. No point pressing at all. You actually have to think on your feet on a constant basis, and there is always something to do, and you are always in danger. Now the draw back is there is no killscreen, but the game is so hard that 99% of players will never play a game that lasts as long as a 3 hour high score DKJr. game.
Now one more thing. I'm not saying that most gamers think DK3 is one of the all time great games, I'm just saying that most gamers can't stand the point pressing involved in DKJr. that is needed for the 1,000,000 point+ scores.
In fact over the years the only reason I believe that most people have chosen DK Jr. to play seriously over DK3 is because Steve Wiebe, and Billy Mitchell gave it their seal of approval by being competitive on it. I believe though in the next 10 years this will change as the King of Kong becomes more of a distant memory I believe the new batch of people will choose DK3 over DKJr. simply because it's funner to play at the highest level.
I could be wrong, but those are my 2 cents.