I have no argument with most of what you've said here, but I'm surprised you've had issues with Jungledisk and large files. What do you mean by "large"?
Jungledisk works great for me, but then, the largest files I have it handle are about 10 MB. Also, the new 2.5 release has some improvements for large files - maybe they've fixed the problem you had?
However, I agree that Jungledisk isn't the all-in-one perfect solution for backups, but my problem is a little different... JungleDisk is very cheap for the few hundred MB in our home directories, but would be rather expensive for the hundreds of GB we have in music and pictures. ("we" being my family, not my company.)
Good 1 TB drives are only 99 dollars now... So I use Jungledisk for hourly automatic backup of /home, which rocks, but external USB/SATA drives for monthly manual backup of /music, which is a hassle.