Just got into an E46M with SMG and I'm loving it! Such a welcome change to have things be easily DIY-able in comparison to my E93 M3. Handling is amazing in it too and it feels so connected to the road.
The SMG transmission might have been a severe problem in the past but with the age of the car (now 12 years old), parts and maintenance items are getting cheaper and cheaper with many alternatives/aftermarket solutions.
I've tracked my E93M with success but now that I have a E46M to play with, I have no doubt that I'll have even more fun out there not having to worry about extreme maintenance costs, and best of all, I can run 17x10" rims reducing my tire costs (as opposed to a minimum rim clearance of 18" on the E9X).
After owning both cars, I can gladly recommend to anyone in saying that the E46M is no less of an "M" car than the E9X... I'd even begin to say that it's an even BETTER car based on what you want and care for.
-Track use, E46M hands down. Relatively light + nimble car and lots of aftermarket/OEM support. Cheaper to maintain and more driver orientated.
-Daily with a bit of track use, the E9X platform is very well-perfected. Awesome technology inside, comfort for DD use and an amazing V8 engine coupled with great handling.
Hope this helps!
2012 R35 GTR BE /// 2008 E92 M3 /// 2013 Ford Raptor