I'm the paranoid type who don't trust leaving data on the phone when I'm flashing ROMs or recoveries.
On my captivate for instance, all the critical data was stored on the internal SD card. It took quite a while to copy the files over to my computer before I felt comfortable flashing.
I also don't like to use the microUSB cables to move files over as the cables can get flaky, so I used SwiFTP to move files via wifi, which is slower but I don't have the cable locking down my Captivate.
Given how I had to flash from rfs to EXT4 on my Epic, realized I needed something back in my old rfs ROM, and then flashing it back to my old DI18 ROM, taking screenshots, data, then flashing back to the new ROM again, it was so much easier just swapping out different microSD cards to get it done, than relying on slow data transfers with the non-removable internal SD card. (I actully had to convert EXT4 back to RFS / CWM 2.5.5, but still couldn't recover, so had to use ODIN to restore my stock DI18 ROM just to restore my NAND back up, so the process was so much easier and comfortable knowing my data was safe on the removable SD card that I had set aside, as opposed to stressing out about it if it was internal to the phone and wondering if it would get accidentally wiped or damaged.)
Just a lot of things that I personally value - security of my data, backing up of my data, all of the important things that I believe a user should do before recklessly flasihng recoveries / ROMs, are made so much easier with swappable external SD cards. My data is more valuable to me than the physical phone itself. I can buy another phone, I can't always buy the data I've spent months collection / creating.
Finally, should I brick a phone, the data on the external SD card is still available to me, not so sure about the internal SD card - if it can be accessed at all if you brick the phone.
Major disadvantages to not having a swappable SD card, from my perspective. And I come from having flashed ROMs on more than half a dozen Android phones and tablets (8 Android devices to date).