I'm not sure what effect it would have on the secondary market, but why couldn't we have a "Core Set," comprised of the basic miniatures everyone needs?
From my perspective, the "Core Set" format has several advantages over the current options (buying on the secondary market or switching to a noncollectable format).
1) Most of the "staple" figures are in the first couple sets. The early sets have a lot of bulky, low-texture figures in garish, clashing colors. As the series has developed, the sculpting and painting have drastically improved, and a core set could have new figures with the same names and stats as the old, ugly-as-sin minis for those of us who are picky about aesthetics.
2) Most of the "staple" figures have been uncommon or common, so reprinting them wouldn't have as drastic of an effect on the secondary market. The new run of Rebel Storm minis also makes me think that Wizards can reprint rare minis, even very rare chase minis, without having their houses burned down by rabid collectors, although I don't think the Star Wars minis market is quite that of the D&D market.
I know that we tend to be kind of defensive about anything that begins to make D&D look like Magic, but doesn't the "core set" approach make sense? It satisfies the needs of those new to the hobby, and helps bring them in. It satisfies noncollectors and casual hobbyists who just want standard minis. But a "core set" approach can also benefit serious collectors by allowing the regular releases to be a little more adventurous with their contents (which is also becoming important as they run out of normal stuff to make minis of). It seems like it would also be a benefit to miniatures players to have a set that's always in print.
As long as they don't do "white base" reprints. Anything but that!