Ah, I did not realise this. I guess it's about finding a balance that suits everyone. The truth is that the majority of people would want easy access to the card to be able to update the files, so alternative solutions would have to be compatible with full-size SD card slots (since it's not really very realistic to produce two different versions).
In my opinion it's better to stick with normal SD-Cards as a matter of convenience. Pretty much every notebook or desktop has a built-in sd card reader without the hassle for searching microsd-adapters and fiddling with small spring or non spring-loaded mechanisms which are prone to break. That suits the majority of people. On the other side i can understand people who want a cart shell without the sd card sticking out. 2 GB RS-MMC is available at amazon for 10 € incl shipping here in germany. Not a big deal.
Home system cart shells are big to a point there's rarely space concern with any normal SD card. I wouldn't count on another version made for microsd. They're already compatible enough using an adapter.
i personally wouldnt care if it had a harddive sticking out the top of the cart! i just pointed it out for those that dont want to modify carts that sd cards are tiny once you take the shell off.
Like I said before, use a Double Pro Fighter for a month, then go back to an Everdrive and see if you still care about something like an SD card sticking up half a centimeter.