Quote "Any advantages to the newer 3 series over the E46?"
Well, the E-90 has an nifty electric water pump that costs about $400.00 as opposed to the E-46 belt driven pump at around $100.00 (parts only).
They both last about 60,000 miles, but by then both cars will need the rest of the cooling system replaced anyway.
The good news is both cooling systems are pretty straightforward to work on.
And then here are the power window switches . . . Al least the E-90 has one switch per window. My 325ci puts two switches in a single unit. That way you get to replace both even if only one is broken. Maybe that's just a two door issue. Anyway, both malfunction at random times, most often on rainy days it seems. Great fun if you have to park on the street.