Retro Studio's games are simply better in every way. Control, graphics, level design, pacing,... they're better games but they should be. The only thing that Rare games did better was the music, which was phenomenal. Also remember that the newer games are significantly longer than the previous games. The reason people are even discussing this is simply nostalgia. Everyone knows the newer are the best, objectively, but there will always be a special place for the original trilogy.
That said, this is the way it should be. It's more advanced hardware and software, and the groundwork has been set. The original Donkey Kong Country series are classics for a reason, and the fact that Returns and Tropical Freeze are so good does them a great service. To claim which is the "best" is largely taste based at this point anyway. I still think Donkey Kong Country 2 is the better game for me based somewhat on nostalgia and theme. I especially liked the pirate theme, but even then if my mood shifts this opinion can change.
Something worth considering though is Returns does suffer a little for me by being on the 3DS/Wii, which means I either have stupid waggle controls on the Wii, which simply ruins a game in my opinion and makes them unplayable, (I actually refused to get the Wii version, as well as New Super Mario Bros. Wii for this reason); or the far better option the 3DS, which still unfortunately leaves me with the problem that my big hands cramp up on the small controls, especially using the shoulder buttons to grip vines as such. It makes extended play harder.
Currently the best in the series is almost certainly Tropical Freeze and that's a delightful fact, it's additional gameplay elements, and the idea of borrowing the Duck Tales style pogo mechanic for Cranky Kong (inspired idea), make for just enough added variety to make it really shine. Really though, why choose? The series is fantastic. Rare did a wonderful job realising it on the SNES and the people who did that have likely long moved on from Rare now anyway, so having Retro Studios take on the franchise and do it such good justice is one of gamings best success stories
...if only Sonic had this much luck.