I tend towards a SATA docking station and seagate 1TB (or less) SATA HDDs. $50 for the dock, $100 or less PER 1TB-ish drive.
I have an old WD 80GB usb drive (with walwart / external power plug). And it mirrors some of your experience. As far as mounting, it takes a little while for USB drives to get recognized. And where / what it's recognized as might depending on what other USB storage devices you have plugged in, or have had plugged in since boot. Check /proc/partitions for the "new" kid on the block if you need to mount it manually. I tend to bypass some of the modern toys like dbus, so my drives get different names if I boot with them plugged in, or not plugged in. And other quirks.
I/O Errors. Yes, my WD gets those. Partially due to old drivers and such. I haven't used it in years. It's pretty noisy to start with so I don't particularly trust it. It also seems to be due to the actual content. i.e. file.tar.bz2 might fail in copying to the drive. The same content in file.tar.gz will otherwise succeed, even though it's a larger file. Which can prove to be a bit mind boggling when all you want to do is use the storage you paid for.
And then there's the seagate 300GB POS I bought all those years ago that has the smart chip issue and NEVER worked right to start with. Even when removed from the enclosure and plugged in as an IDE drive. That was a waste of $300. A big loud CLUNK while using it. And a reboot or power on and power off to use that drive again. For no apparent reason at random it seems. Not really a fan of WD though. My laptop has one in it right now, but it seems to be the ONLY option for drives of that capacity on an old laptop. Anyway, bought that one new. Opened the box and some of the pins were bent, new, from the factory that way. Just two and I bent them back and it fit the laptop. But it runs a bit hotter than any other (seagate) drive I've had in this laptop. I tend to swap out the MAIN drive on my systems once every two years or so, just to be safe. And this WD drive has been otherwise flawless in use. Hotter and noisier, but not a fatal flaw (yet).
Permission issues. I haven't really had that issue. But you do want to make sure you properly umount the drive before unplugging the USB cable. This is not something that happens automatically in a lot of cases. If you don't umount, certain info in the cache can/will be lost. And the filesystem corrupted requiring you to fsck increasingly larger drives these days. Which takes forever, without a journaling filesystem. In lew of manually being able to umount, shutting down will effectively do that step.
USB drives can be tricky in general, because USB is not a guaranteed bus. And disk I/O routines are not geared to handle NOT being successful. As long as you manage it right on the user end, it works out alright, most of the time. But it can be a bit tedious compared to the more traditional internal SATA / PATA (ide) methods of old.