Just got back, diving with Yap Divers/Manta Ray Bay. Friends dove with BTR.
This is just my .02
Yap Divers has EANx. BTR does not. Before I went, I had heard that it doesn't matter cuz the YD DMs made you come up with them if they were on air. Not true. We had most people on EANx, a couple people on air. When the DM/ air divers had to go up, they went up. EANx divers stayed for as long as they want. And trust me, when you are sitting at 75 fsw for 1/2 an hour with mantas, you want that extra time.
Crowds. YD boats are bigger, so they carry more people. BTR boats are smaller. My friends had just the two of them and a DM for a couple days, but then 2 other people other days (and this is just bad luck, but they got skunked on mantas all trip). It's all relative. 6 people on a 20 foot boat or 10 on a 30 foot boat.
The most guests we had were 4 couples, plus DM and video guy. The fewest we had was 5, plus DM. All of the boats go to the manta dive in the morning, so there will always be people on the cleaning station (except when the DM had left us and there were only four of us, until the three boats of Traders Ridge/BTR people showed up). For example, on xmas day, I counted FOURTEEN boats moored up at Mi'l Channel - two cleaning stations, fourteen boats.
Point is, in my experience it wasn't that many people on the YD boats to justify calling then "cattle boats".
In the am, the tide is very low, and the BTR boats have a shallower draft, so while the YD boat have to go slowly through parts of the mangroves, the BTR boats get there a little faster. That is a plus (but you have to come up earlier than those on EANx or go into deco........).
YD is on site at MRBH. So you can eat BF and walk rght down to the dive op, attend to your gear, check on afternoon dives, get gear serviced, get EANx, etc.
Pathways looked nice. Rustic and well put together. It is on a lagoon. Has a decent restaraunt. Have no idea whether you could smell the lagoon at low tide from pathways, I could walking around it.
I preferred being on the harbor, getting a constant sea breeze, thts just my preference.
For some reason I can't figure out, there seems to be an emotional response to this issue. Before we went, I heard people talking about cattle boats, that MRBH is a concrete bunker, too modern, etc etc., like they had to prove how bad YD/MRBH was and how good PW and BTR was. Have to say that none of the things that were said were true, in my experience, is all I am saying. I have been on cattle boats. This wasn't a cattle boat. I suppose if you go at the wrong time and they have a lot of divers, then your experience will differ.
I would say that having heen there, and spending two dives of 40+ minutes at 75-80 feet with mantas soaring over my head, the thing that really made the difference was the EANx (unless you don't mind going into deco).
You can also stay at Pathways and dive with YD.
Whichever one you pick, have a fantastic time.
YMMV, my .02, etc.
Chris