I dont think the series will stand. What got it it's start with KH1 was playing at all the "disney kids" of the era. Bringing all your favorite disney characters into an adventure you could take with them while adding Final Fantasy for a little surprise getting a few of that fanbase in.
For the most part is has been this generation carrying the series. Those either older enough to have started with Kh1 or those that jumped in at 2. And many of us are older now and many more, while loving it to extents, also seeing the growing flaws in story, character development, coherency and so on.
And like discussed in another thread the fun of being in the fandom is gone. Back in the KH1 up to post KH2 days yet pre-Days/handheld days the fanbase was incredibly lively. You had theories everywhere, fun and surprisingly deep discussions on nobodies, heartless, Roxas and so on.
There was so much to delve into, talk about or theorize. It was fun then. But now? Now it's almost dead for anyone that remembers the old times. This site included is a shadow of what it was. In older days it was hard to even log on for the slower internet people due to all the traffic.
I think as far as KH1 or 2 goes they'll stand better or maybe fully stand the test of time even if only for a limited time. KH1 was where it started, it was magical, it played on those feelz, it was simple and it took a creative yet original turn on your favorite movies and characters weaving it into a blended larger story.
Admittedly it had gameplay flaws but as mentioned already it was the first so flaws are natural. In this contrast KH2 was superior on the technical standpoint. Gameplay was smoother, faster, slowed better. It however had it's own flaw in the form of being way to damn easy.
So for these reasons of story (KH1) and gameplay (KH2) I think they'll stand the test of time far better than any of the handheld titles will. Console spreading, the advent of interview quotes, incoherent and so many other things they tacked onto the series and story just makes them poor points to jump into the series at. They took the simple yet magical and fun storyline of KH1 through KH2 and made it a convoluted mess.
Of course for all I know some generation some decade later when all these disney movies come out of the "disney vault" will take it up again as we age to the point of no longer caring but I bet you the games they jump in with are KH1 & 2 while asking "what the hell is Days/BBS/DDD/Coded?" =/