They're removable, so any call to the filesystem could potentially fail at any given time. They're mountable over UMS, meaning an external system can remove the volume you're currently attempting to write, and delete or modify your data by the time you get it back. They're slow, which is hell on a game's startup time, for instance.
The permissions change doesn't really fix any of these problems, but the sugary API they've written to support it certainly makes it a lot nicer to work with. Dealing with all these cases using the File API is not an enjoyable task.
Every single android phone I've owned had the SD card under the battery. That's not going to get removed too often. My current phone (Kyocera Torque) is essentially unusable without an SD Card.
P.S. If there is a setting to tell google play to install to SD card, let me know. I keep running out of internal space because I forget to move new apps.
The permissions change doesn't really fix any of these problems, but the sugary API they've written to support it certainly makes it a lot nicer to work with. Dealing with all these cases using the File API is not an enjoyable task.