I noted a short while ago that I was pretty enamored with Photoshop’s new “Merge to HDR Pro” feature in CS5. I need to reiterate: when it comes to merging the images, there’s just no comparison: CS5 merges far better.
However, after a few days of heavy use I’m really noticing that it’s rendering is… well, passable. But Photomatix kicks CS5′s but all over town.
So the bottom line: for HDR shots that don’t align too well, CS5 is probably better. But your tone mapping will be the poorer for it, unless you can get it into Photomatix.
I’ve wasted far too much time trying to get the images to move over with quality between the two; for now, I post this. In a day or two, maybe more.