I know that many of these opinions are just subjective, but the reason I went with the SR9c were:
Fit my hand a bit better (this was very close).
I like the Ruger trigger much better.
I like the thumb safety over the grip safety.
I found the "felt" recoil (for me) is MUCH less for my SR9c than it was for my XD9.
Finally my XD9 had the "six o'clock" sight picture standard. I like the POA sight picture for my defensive pistols, I also like that the SR9 comes with adjustable sights.
I have no problems with some of the mentioned SR9 issues. Mag disconnect does not bother me, and its easy to remove if you wish. The LCI is big, its true, and the XD's LCI is better; but the Ruger's doesn't get in the way while holstering/drawing and it doesn't get in the way of the sights so its a wash for me. I've seen reviews where the location/size of the thumb saftey can be inconvenient to those with big hands, but with my smallish hands it's in a perfect place and I can engage/disengage with my normal grip with just a twitch of a thumb, but for some I could see that being a problem.
My REAL issue so far has been that I can't for the life of me find any of the compact mags for sale anywhere that isn't on backorder. That and I don't have the time/money to shoot as many rounds through it as I want to