1) Since Google invented "internal SD card" (which is something like dry water), apps that haven't been updated to allow you to choose internal or external SD card are going to default to the internal fake SD card, since it's the first one in Android.
2) Most apps can't be run from external storage. Even if you put the app on the SD card (the real one) and put symlink to tht in internal storage (where Android expects to find it), the app won't run.
3) Get used to it. It looks as if, in bowing to Corporate America, either Google, the manufacturers or the carriers are doing away with removable storage, among other things (like unlockable bootloaders and rooting).
Let's hope a few people come out with Linux ROMs, a few others come out with Linux apps (converting an iPhone app to Linux is easier than converting it to Android, since it's just a different environment, not a different programming language - there have been C compilers for Linux since about day 1 (or maybe day 2), and Google can sell their proprietary system to the large corporations (as secure devices, which would be funnier than any TV comedy show, since open source is always more secure than proprietary by definition).