Short answer is that it's too early to tell.
It really depends on how successful Amiibos end up being and how successful this first line of Smash figures ends up being. If these keep selling, they will keep making them. Alternately, if only the popular characters are selling, presumably they will not reprint the less well known characters.
Also, it depends on how much cycling Nintendo does with the line. Maybe the Smash figures will be gone by next spring and instead they'll have lines of toys based on whatever games Nintendo is selling at that point?
I have been thinking about this topic since these figures were announced. All sorts of Nintendo products have become rare and valuable over time, but it probably doesn't help that they are marketing these directly to collectors. One can't help but be reminded of all of the "limited edition" comic books that were released in the early 90s that never went up in value because they were widely bought up by collectors in their initial run.
There are a huge number of people collecting them in this thread alone, which obviously doesn't bode well. The only thing I really see guaranteeing the value of these early figures is if Amiibos as a thing end up becoming significantly more popular in the future, after this initial run has ended.