Some of these prices seem a bit high for the E46 M3's maintenance. More realistic numbers are:
Oil change every
15k miles: $160 from a dealer. Typical oil change is what, $60-70 for good synthetic every 7k miles? So you're not spending much more in oil and you worry about it less often.
18" 225/45 and 255/40 tires: $700 to 1200 installed, depending on the tire. 19's expect to add another $200.
If something major fails on an SMG car it will likely be a component of the SMG transmission, such as a pump or relay. If it's a relay you're out $10, if it's a pump you might be looking at $1500. The percentage of M3's with SMG related issues is far less than the internet leads you to believe.
You're more likely to over rev an engine and pop it with the manual transmission car. Money shift anyone? Can't happen with the SMG.
Rear subframe tearing. If it's caught early you may be looking at a little over $1k. Again much less common than the internet leads you to believe.
Window motors ($40), sunroof track guides (plastic $5 clips), control arm bushings ($60-100) are much more common issues.
I personally love my SMG M3, especially in the DC area with tons of stop and go traffic. Then on the back roads it roars like no other sub 350hp car can. Plus if you have $2k to spare and don't mind giving up a few luxuries,
not comforts, you could get an E46 M3 near the 31XX lb range.
Now for my comparison to real-world experience with the FRS:
A good friend of mine just picked up a FRS (you can read about it on
http://www.rightfootdown.com/?p=1903 ). We hit the back roads a few weeks ago and damn did it feel nimble. It felt light on it's toes and inputs were instantaneous. The tires were horrible. When driven hard the front end felt it was on the verge of washing out or the rear end was wanted to say hi to the headlights. The engine wasn't necessarily under powered, but certainly was not going to thrill anybody on straight tarmac. The most enjoyable parts of the car were most definitely the response, driving position, and being able to put the right foot down way earlier than most cars when exiting a corner. If I had a BRZ or FRS the first thing I would do is replace those forsaken tires.
For me, I am considering an FRS or BRZ for the fun factor and fuel economy. Mainly the fuel economy, because to me, the E46 M3 is way more of a hoot driven full bore than the FRS or BRZ will ever be. How often do I drive full bore? Perhaps not nearly enough to warrant 333hp over 33MPG.
Ideally you'll drive both cars and reach your own conclusion.