Regarding the API, that's an issue on all of this gen Motorola phones. The problem is that Google has been really advocating doing away with SD Cards all together (the Galaxy Nexus lacked one). Like you said, it is rather annoying for dealing with some apps, and it can make for some interesting situations when deciding where to put ringtones, etc (some apps won't use folders from some places). I think they had in mind that all app related stuff would go on the internal and only Music/Photos/Videos for SD card, since they were banking on people cheaping out and using slow SD cards.
I second the nomination for GO launcher... it really is sufficiently powerful without seeming buggy/slow (like ADW which did more things than I ever figured out, but was also a bit of a resource hog).