I was planning to get an '05 or '06 E46 M3 with about 60k miles and after much searching ended up buying a CPO '09 335i 6MT coupe with 43k miles for about the same money.
I'd read all the same articles, Bimmer magazine buyer's guides, board posts, etc. as you guys had. I went as far as to do a phone consultation with BMWCCA's tech advisor, Mike Miller, who is the author of the Bimmer buyer's guides.
This cleared some things up. Most of the Bimmer articles are written months before the magazine is released. It turns out that Bosch built a new factory in Germany to build HPFP's for the N54... probably to avoid getting sued by BMW over all the trouble they had caused with the Chinese made pumps that continually failed. The latest version HPFP has cured the problem. Notice you don't hear about N55 HPFP failures?
Also, most people tend to lump any vehicle problem in the same "unreliability" category, whereas I make a distinction. A problem (like a MIL light) that it noticed but the car can still be operated normally is a minor problem. Same thing for R2D2 arm seat belt assist not handing you the seat belt.
Getting stuck somewhere with a car that won't run is a major problem. Engine or suspension components failing in use - major problem.
So... in three months and 4k miles with my 335i (including a 900 mile road trip L.A.-Monterey) here's what I've had to deal with:
•Seat belt assist did not grab the seat belt - minor problem - fixed in one day, under warranty
•MIL light illuminated - car stumbled slightly on startup and ran fine afterward - misfire 1-2-3-4-5-6, cause inconclusive - 1 hour in the morning at the dealer
•MIL light illuminated again - two months later - ran rough on startup and deactivated a cylinder - warmed it up gently, stopped and re-started, ran normal the rest of the way. Problem did not re-occur but MIL light stays on.
Took my car in two days later at 8:30 am - MIL was misfire 1-2-3, dealer replaces injectors on those cylinders (leaking) - I have the car back by 6:15 pm.
I consider all of the above to be minor problems except for the injector leak. But even so, my car was drivable and the electronics warned me something was wrong. My total down time was about 16 hours for both problems combined. And both times they washed my car.
***Knock on aluminum***
One thing I can tell you from my E39 experience: When our cars get older, and the price drops lower into the reach of younger enthusiasts, you will notice something: Power trumps reliability for these guys. I had an I-6 E39 which is WAY more reliable than a V8 E39. Not to mention a big difference in fuel efficiency.
But despite all the threads about valley pan gaskets, oil leaks, coolant leaks, fuel leaks, $3000 timing chain jobs on the M62 V8's, whenever anyone put a 540i with Sport package up for sale - especially a 6MT version - guys lined up to want to buy the car. I-6 cars took much longer to sell.
Same thing is going to happen to the 335i's. The N54 is a cult engine. The N54 has it's own website! There will always be someone who is ready to buy your 335i off you when you are ready to move it on.
2009 335i 6MT
(E92/N54), Black Sapphire / Shadowline (Individual 760) / Black Dakota Leather, ZSP, ZCW, 6FL, PDC, no Nav/iDrive, 19 x 8.5 / 19 x 9.5 VMR VB3 in Hyper Black, Pilot Super Sport 235/35 fr 265/30 rr, M3 control arms + tension links (fr)