That's actually a good point. He's into cartoons, that's why Pokemon kinda stuck with me. 

He's into LEGO's as well. Is the LEGO City game worth a buy?

Pokemon might be a bit too complicated for him, try something simpler. Maybe New Super Mario Bros 2 or Mario Kart 7.

If he is interested in the story then he could phase some problems. But if it just the gameplay itself he will learn eventually. I completed Pokemon Yellow as a kid without knowing any English at all, and millions of other kids did the same. Is just trial and error, worst thing that could happen is that he doesn't know what stat moves do, but Pokemon is very easy as it is, so this isn't really a problem.

He might get lost a couple of times, but Pokemon games are pretty straight forward, if you don't know what to do, it doesn't take that much time to get back in track.

How is Pokemon complicated? Unless you compete with real people (that know how to play, there are pretty bad Pokemon players as well), Pokemon is one of the easiest RPGs that are out there. Pokemon AI is known to be extremely stupid, and Pokemon X/Y is no different.

There's lots of text. A 6 year old who can't read it will be very confused and frustrated. Pokemon may be easy but six year olds kids can have a lot of trouble with it. It's best to get him something straight forward that jumps right into the action.  

Get a 2DS, but maybe a less text heavy game like Super Mario 3D Land or Mario Kart 7 would be better.

yup he'll probably spent 10's of hours just messing around, zelda might be good also there's text in it but zelda is more intuitive than pokemon

Certainly get him a 2DS, but not with Pokemon. 3D Land, Mario Kart 7, etc. You said he's into Lego's, so Lego City Undercover might be good, I have no experience with the 3DS version but the Wii U version is fantastic.

I recommend a 2DS. Your nephew might react negatively to the 3D effect! Besides the 2DS is cheaper.

I was playing Pokemon and lots of other JRPG's at his age! To be honest it's a good way to learn a foreign language! I learnt a lot of english thanks to videogames! Anyway Pokemon is a good choice, if you are still undecided you can go and get New Super Mario Bros 2 instead!

Different times I guess. When I was a kid, my friends and I never understood what the hell what was going on, nor what some of the moves did, but we didn't care, we all beat the Elite 4 in the end.

I never knew what Leer does until Pokemon Emerald which was around the time when I start taking English classes.