M3 if it is the coupe. If the M3 is a vert I would choose the 335i coupe or sedan. The E46 will always have beautiful lines and is a very well laid out car in terms of NA power and how well it handles for the weight it overcomes. The 335 can be brought to 400hp by the weekend and would be crazy fun so I totally understand the tight decision.
My vote will be for the M3 but I am assuming it is a coupe.
I had an E46 VERT SMG a few years ago and got rid of it to get my current car (E39 M5), I loved the way it drove but I won't be doing the SMG nor Vert this time around if I do chose to go the E46 route. So it would be a coupe for both options.
Meh, the maintenance doesn't really bother me. It will be hard to find one with warranty and not pay a shit load for it. I've seen a few CPO 335i's with decent mileage and some warranty left but they are in the high 30's. To me its not worth it.
I've loved every M I have owned to this day so I'm starting to lean a little to the E46, on the other hand the E92 is newer and I have never owned a turbo BMW before. As for modding, I wont be doing much to it.. Maybe intake and exhaust and tune if I go the 335 route..