No, not "just plain better." We like them better, hell we love them. But they do have their issues. The biggest one for alot of people is power. The IDI simply has none. Now turbo'ed, intercooled, and with a moose pump. You can break into the 200's in the HP department. That will get any job done, just not quickly. However it's the only vehicle I know where you can replace the entire fuel system for under $1000, and a day's wrenching, then be set for 100k miles.
Cavitation is another issue, alot of these rigs were run for a lot of miles without SCA's in the coolant, and have been pretty chewed up by the block worm.
Also, the return line system sucks. It just does. But Russ (type4) has really really nice return line kits for dirt cheap. If you buy the truck, order one from him the same day. You may not need it right away, but you will soon enough.
Cooling is a big thing for pretty much any diesel, and with the age of the cooling system on that rig, be prepared for water pump and radiator. (use ONLY the motorcraft pump, and the motercraft thermostat for replacements. For the radiator, don't skimp, get a good aluminum one. RodenyRed makes one of the best, it's spendy, but if you haul heavy you'll thank yourself for buying it. The Champion is much more affordable, and ALOT of people here have had really really good luck with it.)
The E40D is often an issue, but proper preventative maintenance usually keeps it on the road without troubles. And while expensive, an updated HD rebuilt unit will be the last trans ever bought for the truck.
The DMF flywheel is another issue, if it's a standard. Replacements are expensive and hard to find, and an SMF replacement comes with its own set of minor issues.
Overall they're ridiculously overbuilt, tough as nails (hell I set mine on fire once... only had to replace the return lines, air filter, and CDR =P), cheap, simple, and they will run on anything that burns. (you will have to add lubrication to your fuel, as they were not designed for the USLD we have now) On top of that, they come with the option of becoming an OB IDI member. This place is the best automotive resource I've ever seen. Both for knowledge and for parts.