Get the Wii version and play it on Dolphin, if you can ;)

Get the 3DS version. The Wii version's motion controls are annoying and DKC Returns seems like a great game to play on a handheld. Plus the 3DS version has some additional content.

The 3DS version doesn't have better controls so much as different - moves that could only be done by shaking the Wii remote (rolling, ground pounds) use X and Y on the 3DS instead. It's better if you're anti-waggle but honestly I never had much of an issue with the shake controls. And there's not a lot of extra content either.

Basically what it comes down to is would you rather play this on a TV or a handheld?

Definitely the 3DS version. There's a really key function in the game (DK's roll move) that you have to use constantly. On the Wii it's relegated to a shake of the wiimote. You often need to use it with really precise timing and it's infuriating having to shake your controller to activate it. On the 3DS it's a button press. That instantly makes the game miles better. I loved the Wii version (it was in my Top 10 games that year) but I'm currently enjoying the 3DS version much more.

So the 3DS version is the same game as Wii's but with a few added levels?