As mentioned already, it's because it was a flop.
The Micro itself was never a bad handheld, but it just got released at a really bad time so it was quickly overshadowed by the DS, which also played GBA games.
Why are they wanted so much? Because they are really nice. It is the true definition of a portable handheld game experience. Plus the interchangable faceplates meant you could essentially 'pimp' it up to look different.
It's kind of like the PSP Go. The GO wasn't really a bad console (Except for some peoples complaints of hand cramps while playing) but it came out at a bad time, and did not offer any real reasons to take it over the other systems released by Sony around the same time (PSP 3000 series).
Usually if the initial sales run goes bad and the item disapears off the shelves, it might be wanted by someone down the track for collectors purposes, or because homebrew/hacking has made it much better than it was at release
