There is no major reason to get the 3DS version over the console version unless portability is a deciding factor(which is a weird way to pick...).
The 3DS version is best as a companion product. It's very simple, and it has many annoying issues. The home console version is sort of the same in a way, but it's larger, it's got more content, it's more interesting, it's got a better story- everything about the console version is better made besides the fact that you can't carry it in your pocket. It's just more fun.
It's clear that the 3DS version isn't a crumb as good as the console version and was made only so you can carry your collection around and occasionally level them, and it's not really a fantastic game. Wait for a sale to pick it up. If you want the game, and you need to choose between versions, get the console version. I mean, they're the same price, so you're essentially just paying for less content if you choose the 3DS version... I know I sound really biased, but it's not great and it's not something I would recommend, and I have my reasons...
Anyway, would I recommend the console version? If you're already a Skylanders fan, truly, yes. It'll be fun going through and seeing how they've tweaked your old Skylanders, so that's a reason to replay them. And it's cool having it just for some of the really good new characters(Bumble Blast! Slobber Tooth!
). You will get bored of it, though that's just something that happens if you play anything enough. Sorry I can't post more detail, I'm just incredibly tired.
If you haven't played the series before, start at the beginning with SA. It's really cheap by now and it gives you a bit more detail on some of the backstory and inside jokes in the game(it's not nessicary to understand the plot, but there are a few times that parts of it are referenced in the next two games). Unless you find it for cheap I would recommend just skipping Giants, it's not awful by any means, but by far the worst of the three and it's pretty dragged on. It's kinda like a filler.