I know I am going to get torched for this but everyone is entitled to their opinion! Stick with the E46 regardless, it's a far more satisfying 'drivers' car than the E9X. I know the E9X is considerably quicker than the E46 but it just doesn't offer the same driving experience. Whilst it's an outstanding car it has lost some of the feel and feedback that made the E46 such a legend, the steering feel of the E46 is second to none and in my humble opinion one of the very best drivers cars ever produced. I have been fortunate enough to own every generation of the M3 and to me the E46 is the greatest. I recently traded back from an MY11 to an MY4.5 because I missed the feeling it gave me everytime I drove it.
In relation to the question about MT or SMG we all have our own opinions again. I have had both versions in the 4 E46's I have owned and both have their good and bad points. The SMG can be costly to repair if abused but in my experiences I have had no real issues with them.
My current MY4.5 is an SMG and the reason I chose it was the color combination, if it'd been an MT I would've been just as happy.
There are also bigger E46 issues to concern yourself with than the transmission and if you'd like to know my experiences over the last 12yrs of owning them PM me.