I have had the same problem. I purchased a micro SD adapter.
Yes: the micro SD cards are a little fiddly to remove, slightly easier to replace as the adapter has a spring action so you know when it is seated.
Yes, the micro SD card does then foul the bottom of the case. A small file, knife, or dremel
removes enough of the case to solve the problem.
I had to replace my SD card holder (techpaul posted this for replacement SD card holders here http://www.raspberrypi.org/phpBB3/viewt ... nt#p215494
: thanks techpaul
I too have a few for emergency use!
Of course a downside (yes there always seems to be one somewhere) is that on a full size SD card you can label the underside of the card (exposed part) and see which card is in the pi. With the micro SD cards that is lost. I am using adapters in my "live systems" and full size in my development system for ease of determining which operating system is in use.