PCGS has never allowed NGC coins in their registry. The fact that NGC did allow PCGS at all is nice but was never required. Most feel the NGC registry is a better community and/or better laid out website for keeping their collections organized.
I own some PCGS coins and almost every one I own is somehow inferior to the same graded NGC coin. Either the PCGS one will be milky or has ugly damaging toning. When it comes to modern US proof coinage all you have to do is look at the population numbers and you can see that PCGS's standards are lower. For some years PCGS has more than 50 graded 70DCAM and NGC still has not seen a single coin that would meet their 70UC grade. I own a 1975 10c PF70UC and also a PCGS version. Side by side it is laughable. The PCGS coin is totally inferior. Also it was about 10% of what the NGC one cost.
This is the case for modern US proof coinage. I can't speak to other sets or series because I don't collect them or haven't done any research.
I bet you can guess what side I am in favor of. I would go even further and remove all PCGS coins from the NGC registry. It will probably happen, someday.