Writers get rejected all the time, and any writer with any kind of track record expects rejection and takes it at face value. While there is some value in rejectology--interpreting the verbage for deeper meaning--it's only worth spending so much time on it. The Magazine of Fantasy and Science Fiction has an informal code to the rejection letters that indicate how far into the story an editor got before moving on to the next story. That little bit is helpful, but not really necessary.
With one exception I will address in a bit, I honestly don't mind any rejection letter, form or personalized. An editor must choose from mountains of stories and many of those are (I'm told) horrible. It should be intuitively obvious that a writer will not sell every story on first submission. Rejection is part of the game, and believe me, it's a numbers game. I have sold stories anywhere from first to twentieth submission. A writer needs a thick skin, which brings me to the one thing that does bristle me in a rejection letter--coddling.
It's one thing to tell me in a terse note that you can't use the story. No big deal--if you don't want to buy it, I want you to reject it quickly so I can send the story elsewhere. However, it's an entirely different thing to say you can't use the story, then go into all the reasons why a perfectly good story might have been rejected. Further, no need to wrap your arms around me and lay my weeping head on your shoulder. I don't need you to tell me to keep writing, keep submitting, maybe somebody else will buy the story. That talk is for rank beginners.
That rejection letter might be just what a beginning writer needs for motivation, but it makes an experienced writer's eyes roll. So please, please generate a second form-letter. If in my cover letter I list a professional sale, just tell me you don't want the story and move along. A 1/8 sheet strip of paper is plenty for that.
If you are taking the time to hand-write a comment, it means I was close. If you aren't going to do that, I really don't care why you are rejecting the story. Just tell me so I can move on to the next one in line. Don't try to coddle me, that is insulting.