Steve:
The rod bearing issue (and it is not isolated to one engine family) is sort of funny to me.
Why?
Because it only happens on the high performance versions of the engine family.
So, the M54 for example, doesn't have the problem, whilst the S54 in the M3 does.
The M62 doesn't have the problem, whilst the S62 has been known to have rod bearing failures. Though I don't believe in the same degree as the S54 did.
What I find even funnier is that the Unicorn Urine (Castrol TWS 10w60) that these engines supposedly "need" to have doesn't stop the failure from occurring. That is part of the reason I didn't bother with TWS in my car.
And of course the more pedestrian engines don't require the special oil either, just the typical euro 3.5+ HTHS stuff.
As far as spotty quality and expensive repairs? You only get raped going to the dealer. My M5 hasn't been overly expensive to own thus far, and parts for my sister's 330i are cheaper than the ones for her Explorer.
Build quality, fit and finish, quality of interior materials and the RIDE, that's what makes them desirable.
But they DO have their quirks! Just like every other make. The fact that the most severe of these quirks (the rod bearing issue) happens on their "performance" models is probably the reason for the harsh criticism.
Nissan had transmissions that lunched on the GT-R
GM had the self targa-topping "feature" on the 'vette
Ford had failing LCA's on the Ford GT
Those are the "performance model" issues I can think of off the top of my head.
Non-performance model failures, we end up with a much larger list:
Ford: transmissions on their FWD platform, spark plugs ejecting (modular), spark plugs breaking off (modular), cruise control pressure switch fires.
GM: Dexcool sludge, intake gaskets lunching themselves causing potential engine failure, piston slap, excessive oil consumption (Saturn), transmission issues (Cruze), timing chain failures (Cadillac), head gasket failure/head stud failure: Northstar....etc
Dodge: Transmission problems (vans), intake valley leaking (318 IIRC), sludge (4.7L), differential failure (RAMS), transmission failure (RAMS), steering boxes falling off (RAMS), "death wobble" Jeep and RAM's....etc
Toyota: Severe engine sludge causing failure, frame failures, self-destructing camshafts, the unintended acceleration fiasco....etc
Honda: Oil filter fires, transmission failures, ignition switch fires, engine sludge (MDS odyssey: Trav's documentation), body corrosion
Nissan: engines dying due to consuming catalytic converter material
The list goes on and on.
You are right, there is an internet amplification effect going on here. These are VERY expensive vehicles (M-series cars) that are having this problem. THAT is why it gets the recognition it does.