Fuel atomization in diesel engines differs from your average "el-cheapo" garden variety GDI engine, e.g., my 2018 Hyundai 2.4L Theta II mill. GDI engines are terrible when running rich. Some manufacturers added port injectors to the intake manifold to remedy the situation.
On a D60 you have to replace the EGR cooler every half a million miles or so, depending on a few factors. It can be cleaned, but it's not worth the effort as the cleaning is not as good as installing a new one.
Yes, EGR coolers are one thing to mention for sure. Same with EGR build-up in the intake ports and in the turbo. My buddy's 6.0L PSD killed multiple EGR coolers (he was running a tune) and when he pulled the first one off, the intake was filthy. Cleaned it up and he eventually deleted the EGR, which made a big difference on fuel economy (picked up an instant 2mpg) and how long the oil stayed clean.
We have one completely pre-emissions diesel still in our fleet at work and it is universally less problematic than the EGR engines. The most problematic is actually the 2nd newest, IIRC, the truck is a 2011 Freightliner with a Cummins ISL in it, which is pre-UREA and has had many intake/exhaust related issues like turbo failure, EGR blocking, and associated equipment and other weirdness. The newest is a '19 Kenworth that's been problem-free so far, the oldest is a 2000 Freightliner with a non-emissions kitty-CAT that's been bomb-proof. We also have a like 2008? Freightliner with a Mercedes, and it's been mostly good, no DPF IIRC, not sure if it has EGR or not.
Sample sizes of 1 I know, but my buddy that used to wrench on busses and now manages a fleet of 150 of them (he owned the PSD) says that universally, the pre-emissions diesels were less problematic and got better fuel mileage and EGR was the biggest PITA with them, particularly when the companies were trying to avoid DEF/UREA and so experimenting with EGR things. CAT's ACERT was an interesting approach there.