Get Manual. Then, you have one less thing to worry about, the hydraulic pump.
However, last month in 8.5 years, I replaced my first clutch at 82,000miles.
Mine is SMG though. Apparently, I drove with my worn out clutch for the past 32,000 miles. I thought it was just my car making noise after two rear end accidents. When it started slipping very badly last month, I changed it and the noise was gone. I'd say BMW clutch and flywheel are pretty solid. The mechanic was really surprised how long the clutch lasted.
Very last point, check if the E46 M3 you're buying has subframe reinforcement or not. Back in 2008, I was naive to believe the 1st bodyshop owner's words that he will reinforced my subframe while fixing my subframe from my car accident. Afterwards, my subframe cracked pretty badly to the point there was a 6 inch gap to both sides.
If you find a nice E46 M3 you like, reinforce the subframe, it will only cost you $1000 tops, but this is the CDN rate.
Due to my bad crack, I paid up $3000 to have it welded back again and reinforced. I should've had my car checked when it was finished repairing. NEVER believe a bodyshop's words. I was too young to believe people. REMEMBER to CHECK!