It's rather interesting how the different manufactures seem to keep having the same issues, to the point that if I hear of a problem I can guess - with pretty good accuracy - which manufacturer is having the problem. Inclement weather - GE/CFM: Fan flutter and bearing problems - Rolls: Compressor stability and compressor case distortion - Pratt.
Yes, the takeoff surge was a wear-out problem - the reason the problem with the PW4000 went on so long is that Pratt didn't want to spend the money to fix it right. So they kept trying different inexpensive band-aids that were not effective (hence the song and dance to convince the Feds that the risk of a dual engine event was infinitesimal). It was only after the dual engine event that the FAA said "FIX IT" - yet again they tried an inexpensive band-aid with Cutback stator which failed miserably. P&W could have saved a fortune if they'd bit the bullet early on and did the proper compressor redesign fix, but the bean counters wouldn't allow it so instead of spending what it took for a proper fix early on, they ended up spending much, much more later on.
With respect to the PW6000 - according to some of the people I worked with at Pratt, the designers warned early on they were trying to do too much with the compressor but management wouldn't listen. There is design trade in compressor design - the less stages in the compressor for a given compressor pressure ratio, the smaller, lighter, and more efficient the compressor will be. However it means pushing each stage harder which means reduced stall margin. As compressors wear in service, they lose stability margin - so what might work OK when it's brand new can become a problem as it ages - so you need to design extra stability margin when it's new so it'll have a long on-wing life.