The timing chain failures mostly seem to be from SOME of the D40s. Despite it being nearly the same engine in the 2.5L STR D22, I've heard/read very few reports of any major problems with the D22.
In reality it's not a large percentage of shipped cars that have the failures. It's difficult to pick why it's happened - that's one of the reasons I started that poll on the choice of oil filter in relation to timing chain failures. That proved to be a mixed bag as well - some reporting that aftermarket filters have caused no concerns, others reporting failures with genuine filters only so while it's not conclusive, it does make me personally lean towards exclusively using genuine filters ... but I digress.
The Renault-designed 2.5L engine is quite robust except for the possibility of the timing chain going. I can't imagine why they didn't use HyVo chains in there - my 1977 CB900 had a bloody HyVo chain driving the camshafts.
I've heard of complaints about the injectors - not many, but some - and they're bloody expensive from the dealer but much cheaper if you buy them aftermarket (I think Baileys Diesel Group do a great deal on them). You have to replace the spill pipe gaskets at a minimum, Nissan will advise you to replace the high pressure pipes as well (which might be a good idea if there's any sign of damage on these).
The SCV is not so much a failure point but it gets dirty - and that makes me wonder three things. First, how does the dirt get past the filter, and second - why was the SCV designed so that it could be interfered with by debris? And, is there a way to improve that? Don't know, and Nissan obviously won't be doing much about the YD25 as they've already moved on.
Other than those faults - you can't really knock the engine itself. It puts out a fair amount of power and torque for its size - although the new NP300 powerplant, despite being smaller, gives it a good run for its money. Speaking of which, I wonder how far you could take the 2.3L engine out in terms of HP/T by changing turbos, intercooler(s), water/alcohol/gas injection etc etc. The YD25 gets quite a bootful - one member here has increased the output of his YD25 from 96kW to over 150kW. Will we see 50%+ gains possible from the NP300?