This seems to be a recurring comparison, which speaks highly of the Macan, considering what segment it's supposedly in.
The M3 and Macan were my two top choices (M3 because I need the extra headroom over the M4, plus IMO the M3 looks meaner and cooler).
The drivetrain of the M3 is what I really want. But is it worth that price? I have a 535i M Sport now, and the 3 looks similar enough to where I think it shares the most beautiful Sedan design language right now. However, for me, I would never be able to use that glorious I6 enough to justify paying THAT much for a 3 Series. The Macan on a refinement and interior scale comes across extremely different enough to seem several classes above. I mean the 3/4 interior is CHEAP, very low-rent, rental car grade, even with the nice M seats and rare bits here and there (unless you get leather package, taking it into really expensive pricing territory, and it'll still come way behind a Macan or 5 Series, etc. You can't even "sync" both sides of the HVAC on the M3/M4, as it uses BMW's low-rent HVAC unit (not the one that comes on the 5+ cars).
To me, the Macan was just a superior overall package, enough performance, and shines above the M3 in more ways than not. Also, the M3, although stunning in its own right, is still a "3 Series" and I guess it's hard for me to get past that. They're everywhere, with ugly halogen headlights (M3/M4 have ugly halogen taillights! Crazy to spend $70+K on a car and be stuck with those retrograde things). The Macan is a more interesting and unique, special looking car to me (in SD Package or Turbo form, namely). Also, it's a Porsche, and the only Porsche that I can actually comfortably fit in, so it fits a big dream-car aspiration I've had my whole life.
To me, since I won't be tracking the cars or able to exploit the M3's race-bred virtues, the Macan is just worth the money more than the M3. Especially since the M3 actually came out to more for me. And Porsche has earned my trust to be the only brand I'd actually BUY a car from (not lease), as they treat their brand with respect and acknowledge that the way their used cars age has a lot to do with how their new cars will be regarded. So I think they'll protect the Macan's lineage in terms of resale more than BMW, who always find themselves stuck in the highly-incentivized lease rat race, which diminishes the value of their cars both tangibly and emotionally. The M3 hopefully will be treated with dignity in regards to supply and incentives, i.e not overflowing them so it can retain a strong resale, but I think the Macan should fare better.
Oh, on another note, while I feel that the M3 would be more fun to get into and drive every day, that might get old quickly as the harshness and lack of refinement set in. I feel that the Macan will provide a more premium experience whilst holding onto fun-to-drive sporty dynamics, have a higher sense of occasion, and of course, give me the warm and fuzzies every time I look at it, registering that I "made it into the Porsche club".