Your version of android is Android 4.3 = Jelly Bean which I could not test on my nexus 5 which runs Android 4.4 = Kitkat by default and their are no roms (custom) that are below kitkat and makes no sense to make one.
I did a test with my older motorola triumph and did testing with jelly bean and again, no problems using MTP.
Your wife's phone works, yours don't, and I really can't find anyone using your phone having problems with mtp and linux (a few dozen with windows) and I see last month you had a post at SolydK with the same issue.
If the phone was mine, I would do a backup (nandroid, etc) and do a factory reset and don't install any apps, stay stock and try mtp again, but, that way is not for everyone, depends on how good you know your way around android.
I really don't think it is a debian/siduction issue.
The only other simple thing I can think of is switching it from media device (MPT) to camera (PTP) and back again (in settings)
I have no further advise or ideas