I just installed a new AP. One piece of advice I was given a while back and that was "Keep it in the family." Meaning if it is Garmin, then AP is Garmin or Raymarine etc.
A few years ago I chose Raymarine. Easier to connect and talk to all your different displays.
I hear this same advice all the time, but really don't agree with it. I think it comes from installer who are either lazy and want as simple a plug-and-play, then walk away job as they can get, or installers who don't know what they are doing well enough to implement more complex systems. And they really aren't that complex.
Maerin described interfacing and chart plotter and AP really well. Attention to detail is key, and that typically translates into time, so I can understand why techs don't like it. NMEA 0183, though primitive, is absolutely rock solid reliable when installed correctly. There is a reason why it's the only accepted interface on IMO vessels (ships and passenger vessels).
I have all sorts of different vendor products connected on my boat, and it works perfectly. The interfaces are open, standardized, and well documented. That said, various vendors have implemented supplemental proprietary interfaces, largely with a goal of getting you to think you should stay "in the family". Seatalk is an example, but I think all the vendors have moved to 01830 and/or N2K, and do the proprietary stuff that way and with ethernet. Vendors also create glitzy features to motivate you to stay in the family. If that stuff is important to you, then by all means stick with one brand. But the down side is that if part of the one-brand package is a lemon, you can find yourself replacing everything, which again is just great for the electronics manufacturers.
Getting back to this situation of a failing AP, I don't see any reason why you can't replace it with whichever AP you think is best, regardless of brand. You WILL need to look at how it will connect up. How many 0183 ports (if any), N2K, etc.? But that's part of any good installation.