It's not what happened IN the engine, it's what else is bolted ON to the engine. The issue with the emissions is basically the exhaust - the exhaust needs to be cleaner (fewer emissions, less/smaller particulate matter.) In order to get cleaner exhaust, engine makers have done all sorts of funky things.
One of the solutions is to add DEF to the exhaust stream (Diesel exhaust fluid, or urea - a mild acid I believe) - to chemically help neutralize some of the emissions.
Another solution is sometimes to re-circulate some of the exhaust gasses back through the engine, helping it burn hotter, to get a more complete combustion cycle.
All of these extra systems are just that - extras. More parts, more hoses, more complicated routes for hoses and lines to snake across and engine bay. There's more "stuff" to break. Some of these systems also have complicated sensors (and engine computers), which are just by nature harder to tweak/adjust - you can't just turn a screw or replace a spring to dial up the power a little bit. Some of the old engines would literally run until they ran out of oil, or some imbalance shook the innards of the engine apart and sheared something apart - the modern engines will shut themselves down or go into limp mode if the detect a fault with a sensor.
In some ways, you could summarize an old diesel engine this way :
Fresh air in the front -> Heat/noise -> POWER!!!! -> Exhaust out the back
Now its more of a giant squiggly line with computers, sensors, DEF, EGR valves, mufflers, more computers, and a whole bunch of wires.
I don't think any manufacturer has come up with a particularly good system - I'd equate it to the early CFL light bulbs from 10 years ago when people began to think about being "energy efficient." A lamp is a lamp, that hasn't changed - but the bulb has. CFLs took forever to warm up (and get to full brightness), they got dimmer over time, didn't like the cold, and the color temperature of the light itself was often pretty bad. Forget using a dimmer. Now we have LEDs, which are cheaper, sturdier, and provide light that looks just like a standard light bulb, and cost only slightly more.