N54 had issues like high pressure fuel pump, wastegate rattle, water pump, injectors, carbon buildup and some other minor stuff. The engine itself is basically bulletproof, it's just that much like most other German automakers, BMW over engineers stuff and the complexity of the electronics is what gets you. My '07 is relatively low mileage at 44K and no major issues for me. I'm well out of warranty but don't have any real hesitation about driving the car, I'm not afraid it's going to strand me. I get random error codes like bulb checks, but nothing that I worry about. A lot of the N54 stuff had extended warranties on like the turbos and HPFP so most of the lemons were fixed.
N55 fixed most of the N54 issues, but it's also limited in terms of power potential. If you don't plan to really mod, it's fine, but the N55 went down to 1 turbo from twins. And the N55 has VANOS issues, I'm fuzzy on the exact issue, but they can fail and that can strand you. Also, they have the same electronic water pumps that N54's have and basically all BMW's. It's not a bad thing in that the water pump is really advanced and can stay on while the car is off to cool off the turbo after driving. But unlike a belt driven pump, when it fails you're stranded. There is no real warning, it's fine one second and then the next you've overheated and call the tow truck. It's not as common as some say, but I would be mad if/when it happened to me.
Maintenance isn't bad if you can do it yourself. Parts aren't any more than the FX and it's not much more complex. There is much less room to work since the engine bay is a lot smaller. And BMW basically makes you remove everything to work on it. Last year when I had to replace my AC condenser due to a leak (aftermarket oil cooler punched a hole in it) I had to pull the bumper, intercooler, radiator, fan, engine cover and a few other misc. parts just to get it out. On the FX, there is so much room I could have just tilted the radiator back and slid it out. But for maintenance stuff like spark plugs, it takes 30-40 minutes just like the FX and no longer for an oil change.
Is the BMW annoying? Absolutely! But for me, it drives so incredibly well that it's worth it. Of course I haven't been stranded by my 335i yet or taken it in for a major repair, so maybe my attitude will change then. But if I would sell the FX before I sell the 335. FX is more reliable, but the driving experience isn't the same. I will probably replace the FX with an X5M when it comes time.
And I'm guessing you're replacing your IS w/ a 335? FWIW, I had an '06 IS350, got it a month after they came out. I loved that car, it was fast, handled well, was comfortable, and super reliable. I will say that other than reliability, my 335i is better in every way to me. It's faster and just drives better. Transmission shifts quicker, the paddles actually work and steering feel is better. The only thing about the IS350 that I miss is that I never once thought about reliability. I knew it would always run perfectly. BMW is way more temperamental.
