Ive owned both ZF5 and E4OD 7.3s and I dont prefer either one. The E4OD seems to be tougher and I have seen people put way more power in front of a stock E4OD than a stock IDI ZF5 without damaging it. The only real problem I have had with an E4OD is that the stock cooler is kind of small if you tow long and heavy. Upgrading that is fairly cheap and easy and can preserve the transmission far beyond what people would expect.
The biggest issues I have seen with it is when people dont maintain them at all. People tend to think you just run it till it dies and dont realize that you do actually have to perform some minor maintenance on them over the years. Checking and Adjusting the TPS makes a monumental difference. Changing out the fluid and filter and replacing the Torque converter when youre supposed to are both very important. Just like a clutch, they dont last forever and if they go, they tend to take the whole unit with them.
My Superduty has had an ATS triple-lock TC in it since 2014. Stock TC seems to have been replaced around 150k and it now has 228k on it being worked in a quarry and now hauling logs and landscaping materials. It does an excellent job but I also keep up on routine maintenance. When I got it, the TPS was pretty far out of range and it was causing issues with shifting, the OD light would occasionally blip on for some seconds and then blip off. New sensors adjusted into range solved that and it hasnt come back in ~10k miles of hauling.
These are tough transmissions, superior to most other brand offerings at the time. They have no inherent weaknesses (except, maybe the cooler size) and they will last a long time as long as they are maintained properly.