Gen 2 AC Compressor Replacement: Toyota or Aftermarket?

My wife had her Prius Gen 2 (2005) AC compressor replaced last September with a non-OEM AC compressor. This year already it didn't seem to be very cool, so we took it back to the independent mechanic who replaced it. They checked freon and said it was low, but found no leaks. They recharged it, but cannot explain why the refrigerant was low. The car cools acceptably now, particularly since I replaced the cabin filter, so at least part of the cooling problem seemed to be a dirty cabin filter. But AC on my gen 3 Prius (2011) still seems to cool the car better than the AC in the gen 2.

I doubt the engineering is that much better on AC systems between Prius gens 2 and 3, but that's the first question--is the gen 3 AC system better? And the second and more important question: The mechanic is willing to replace the aftermarket compressor they used with a genuine Toyota compressor. since their repair has a 3-year warranty. My next and more important question: Is there a significant difference in part quality between OEM and non if it's a reputable shop? I have no idea what brand was used, so I suppose the question is whether the genuine Toyota part is likely to be superior generally.

Thanks in advance for any insight.

 

They are offering to put it in for free. They said after the recharge it seemed to them that it was OK, and they didn't get any codes so they thought the low freon was the only issue. So they suggested I try it as is, but when I picked up the car after the recharge, it was still blowing coldish but not cold air. I called them immediately and told them I going to bring it back for the replacement. But since I couldn't get it in before the holiday, I though in the meantime to try replacing the cabin filter, which to their credit they said neded replacement although they didn't connect it as a potential cause of the AC issue. And the reason for my question is that even with the cabin filter the AC mostly works but still seems it could be better, possibly with the complete replacement they are offering. So the question now was going to be, given an offer of a free parts and labor replacement to a Toyota OEM part, should I do it? And I suspected the answer would be yes even if things are working OK. As far as the mechanic knows, I am electing to go forward.

Part of my concern was that before the complete recharge they said the compressor was noisy, which is why they were going to replace it. They said it stopped making noise after the recharge. I Have wondered all along how the freon could be low a year after a compressor replacement. If there are no leaks but freon was low, would the issue likely be the compressor?