I couldn't find any official reason for the Kremlings' absence, but I would guess it just has to do with changing times. The most recent DK games released before DKCR involved musical instruments. Nintendo and Retro probably wanted to tie that into DKCR, which is why most of the Tikis resemble instruments. I'd also say Nintendo and Retro probably decided they didn't just want to make another version of DKC and do exactly what Rare did.
As for what will happen in the future (I miss the Kremlings too), the Tikis have since appeared in other games (most recent being Mario Kart 7, which came out in 2011). The Kremlings, on the other hand, haven't appeared in a Nintendo game since 2008.