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I'm selling my 2004 330i ZHP, which is as close to a 4-door M3 as you could get from an E46. The car has been in my family since it was new, so I know fairly well the issues with E46s relative to the Toyobaru twins.
The big issue you'll have is maintenance. While some things are well within the realm of a good driveway mechanic (I did my last brake job in my driveway for about $300 in parts costs), other things (like the inevitable VANOS rebuild) are not. And of course, since it's a BMW, parts costs and service rates are higher. The E46 range was plagued with issues from subframe separation (catastrophic) to weird electrical gremlins to unusually terrible window regulators. Any E46 you find will have pretty high mileage, meaning you'll want to verify that things like the water pump have been replaced.
If you want a comparison between the cars themselves, they're very different. Even my 330i has a lot more torque than my FR-S. An M3 will obviously have much more power than the FR-S. I notice the difference in torque all the time in daily driving; you can't just floor the throttle, you need to downshift. Fit/finish and materials are in a totally different league. The FR-S has a decent interior for a $25k car, but not something you'd confuse with a $60k car (even a 10 year old one).
If you're at all on a budget, I'd lean toward the FR-S. The maintenance, gas mileage, insurance, etc. will all be higher with the M3 than the FR-S.
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