This is exactly the choice I was making. Initially I was looking for an E46 M3 coupe or perhaps a Z4 M Coupe. It was very difficult to find late model low mileage E46 M3 even in California. I was looking for a E46 M3 that was a 2005 or 2006 model year with not more than about 60k miles. There were very few around, especially the '06 (mostly convertibles). Prices were $28k-33k.
I had to look at dealer cars because I needed to finance the purchase. That also restricted me to '06 and newer due to the difficulty in financing older cars.
Now add to that: The few cars I did find were all SMG. I knew about the SMG pump issues and the very costly clutch replacement. I had not (and still have not) talked to a single SMG equipped M3 owner that had anything good to say about that transmission. I know one guy that swapped his M3 from SMG to 6MT.
The only 6MT E46 M3's at a dealer were at Enthusiast Auto... in Ohio. Just too damn far from SoCal.
Since there were no more CPO E46 M3, I needed to find a car with a good maintenance history and clean Carfax. Not too many owners, non-snow states only. I didn't find anything locally. When I found M3's at dealers out of state, they were frequently slow to respond to my e-mails and could not come up with documentation on the cars they had.
Looking at CPO 335i was my back-up. I wasn't really taking it that seriously. Most were overpriced (in the $35-39k range) and about 99% were automatic. 335is were rare and usually around $45k.
Then I found my car: '09 CPO 43k 6MT, no Nav, iDrive or Premium, 19" ZCP style wheels, etc, obviously an enthusiast's special-order car. It was at a BMW dealer in CA but 600 miles away. Carfax was clean (2-owner), dealer e-mailed me the service records. HPFP had already been replaced.
They even delivered it to me in an enclosed trailer...
True M car
Simpler engine (NA)
Limited slip diff
Better suspension tuning - no run flats
Engine has similar HP more torque (stock)
Drastically better tuning possibilites
Better fuel economy
Available with CPO
2009 335i 6MT
(E92/N54), Black Sapphire / Shadowline (Individual 760) / Black Dakota Leather, ZSP, ZCW, 6FL, PDC, no Nav/iDrive, 19 x 8.5 / 19 x 9.5 VMR VB3 in Hyper Black, Pilot Super Sport 235/35 fr 265/30 rr, M3 control arms + tension links (fr)