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Both nice cars with similar interior space. I like the looks of the E46 a bit better, but it is about to become 2 models removed from current...(plus a e93 refresh) if that makes a difference from you. Obviously the N54 motor out performs the M54B30 by quite a bit.
Interior... From the factory, the seating and leather are a bit nicer in the E46, and the car is a bit bigger (by nearly 10"). However, the E88 seats are 2 years newer, and will likely show a lot less usage, and the E88 has the M Sport Package, so it might be a bit sportier in that car.
The suspension if quite a bit more sporty on the E88, and the E46 is a bit more floaty.
As mentioned, there are issues with the HPFP on the N54, that is covered under warranty through 100k miles on that car.
They both get about the same gas mileage, with the tip of the hat towards the E46 if you dip into the turbos more than normal.
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