Nintendo stated some time ago that the NX is not going to replace the Wii U or the 3DS, and that they will continue to support both even after the NX has launched next year. The Wii U is in dire need of replacing because it's utterly dead in the water, but the 3DS is still going strong and I expect it will continue to for at least another year or two, even if the NX is another handheld...which seems doubtful. Popular theory suggests it will be a hybrid between the two, but we've got nothing but speculation to go on at this point.
Now, it might be worth waiting for the supposed upcoming announcement (whenever THAT is going to be; like all things NX Nintendo remain infuriatingly uncommunicative) to see what the NX is, and if it can play 3DS titles - I doubt it, but you never know - but I'd say it is still very much worth getting a 3DS at this stage even if it can. There are plenty of titles coming out for the 3DS in the near future, and it has a solid library at this stage, so if nothing else you'll have plenty to catch up. Plus there's the DS backwards compatability as well.
As for the differences between the New 3DS and the regular 3DS...the New 3DS has an analogue nub that serves as a mediocre substitute for proper dual analogue (it's highly responsive, but very stiff and awkward) and has an improved internal processor that means games generally run smoother, although it's only really noticeable in titles like Hyrule Warriors Legends. It has two exclusive titles: Xenoblade Chronicles 3D and The Binding of Isaac, the latter of which is eShop only. It can also run SNES eShop titles, although the library for those is pretty small at this point as they only started releasing them this year. The stereoscopic 3D is also much more stable - to the point that's actually useable - on the newer models. That's pretty much it. But you're definitely better off with the newer model; better to have these exclusive things than not, especially when the price difference is so minimal.
That said. If you're worried about the NX supplanting the 3DS - it won't, but even so - and don't want to fork out a lot of money - and don't care about the exclusives the N3DS offers - you could just get a 2DS. Chances are you won't use the 3D (trust me, you probably won't; nobody does) and it's substantially cheaper, especially with the recent price drop in the Americas. That way you can experience the titles you're interested in and still save a lot of your money. A 2DS would cost about half the price of that bundle and you could probably get a game in the bargain.
tl;dr - I say yes, go for it, get a N3DS (or a 2DS if you're money conscious) and NX be damned, because it's highly doubtful it will be a pure handheld system, and if it's not backwards compatible it's going to take years for it to build up a library to justify buying it...these things always do.
You've got 5 years' worth of 3DS games to occupy you if you get a 3DS. Hop to it!
