I just picked up an M9 yesterday, and my overall personal choice would be the S6. The camera performance on the S6 is just so much better than the M9 in pretty much all aspects. You know a camera is good when you want to take more photos of things. Whereas my experience with M9's camera is the complete opposite. Even if I took the image in RAW mode, adjusting all the settings to get the correct exposure, etc, then export it to photoshop to manually touch up the images... even then... the S6's camera could take the same shot in full auto mode in a matter of seconds, and have a photo that looks better than the M9's.
Full res images for
One M9,
Galaxy S6,
Note 4,
Nexus 6,
Lumia 1520 for comparison if you guys are interested.
Battery life between both devices wasn't that far off for me personally. The M9 lasts longer for sure, but not by a sufficient margin for me to completely write off the S6.
Speaker quality on the M9 is unbeatable, but I listen to music more often on earphones, and S6's wolfson DAC sounds much better to me. In fact on earphones, I couldn't stand Dolby's EQ at all. Turned them off immediately.
In the past HTC has a huge advantage in build quality and the premium look and feel. But Samsung has come far enough for me to be okay with the S6. But the One M9 definitely feels more premium and well built to me.
I prefer Sense UI over TouchWiz hands down. But again, Samsung has made huge strides in optimising the UI. And I can certainly live with Touchwiz on the S6 (with more Samsung things turned off of course.)
Performance on both phones feels just quick, though the S6 felt faster loading apps and games, probably because of the faster memory. But not a big deal to me. Both phone performs really well.
Screen on the S6 was much better in my opinion. Better contrast, better outdoor visibility (brighter), able to go super dim (for using at night in bed), better colours too. Pixel density is not a huge deal to me, the M9 looks just as sharp when i'm using both phone at normal handheld distance. But the M9 display's colour seemed a little off to me compared to other IPS panels. Particularly the blues and the greens. Like app icons' colours are fixed across all screens, but the Hangouts and Ingress icons' colour looks "blown out" on the M9.
The bonus on the S6 to me was the home button. I've never really liked it in the past, but this time round the button brought enough to the table for me to consider it a pro. Fingerprint sensor actually works properly now, not to mention the camera launch is really consistently quick.
In the past I've always preferred the HTC option. The One X, the One M7, the One M8. But this year... the S6 has my vote.
Depending on your needs and preferences you might come to a completely different conclusion and choose the M9 of course. It's still a really good phone.