I can't really compare Mercy & McKeesport directly for you, but it does seem that UPMC & the medical school are putting more resources into Mercy than they are into McKeesport at the moment. Pitt Med students are now doing a variety of rotations at Mercy, which even as recently as a year or two ago was not the case (and, with the possible exception of family medicine, I don't think there are any rotations for Pitt medical students at McKeesport). Some of the physician groups work both at Mercy and at Presbyterian/Montefiore/Shadyside, while I don't think I know of any that also work out at McKeesport. It seems like there are more sick patients that stay at Mercy, while a lot of the more complicated/sicker patients at McKeesport will be transferred to Presbyterian/Montefiore. Mercy also has a few unique centers within the UPMC system - all of the burns and most of the rehab patients are sent there.
All of that being said - the IM residency program at Mercy is still much, much less competitive than the Presbyterian/Shadyside program.
One thing to note though, if you are considering applying to Mercy - it is still a Catholic hospital, and many of their policies regarding contraception/abortion/end-of-life care reflect that. The sense that I got from some of the clinical and non-clinical staff while I was there is that it has liberalized somewhat in the years since it became a UPMC hospital, but it is still certainly much more conservative in that sense than the other hospitals in the area.