I got both an E90 M3 and a 1M (both 6MT). And until very recently I also had an E46 M3.
E90 M3 vs 1M is very close.
I personally can pull about the same times on our local track maybe a second faster on the 1M. At this altitude (2,240Mts above sea level) the 1M will leave the M3 easily behind in any acceleration situation. But, the M3 is easier to drive at the limit (this is a fast track, not a short one) because the throttle response is two steps above the 1M and the chassis is more neutral and less prone to snap oversteer. The 1M is much twitchier, a lot of fun, but it takes an expert and/or ballsy driver to really take it to the limit on corners. The M3 is a lot easier. I have some driving skills, like a good amateur but not a pro (been to multiple schools).
Any difference in performance is academic between these two, any driver difference will be greater.
Most fun? The E46 bested them both
but it was very noticeably slower (3-4 secs/lap). The 1M is really close in fun, the M3 maybe a half-step behind.
For daily driving the 1M is a lot more fun than the M3 because its power curve is so much more useable.