I realize this is a little late, but why was the hardware MUX fail-safe removed going from APM1 to APM2?
It didn't do anything we couldn't do in software on the new 32U2 chips in APM2, and we wanted to lower chip count, cost and complexity. The software MUX has been working great.
The PWM output to the servos is still through the 2560 though. Even before we started modifying the APM software for our own uses, we couldn't prove that the APM core software can't encounter a critical exception. One of our teams made their own hardware fail-safe with a PIC and a MUX; it looks like we're going to have to do something similar to pass safety review in the future.
Most people use APM 2 for copters, which cannot be controlled manually, so a direct PWM pass-through doesn't make any sense. For planes, APM 1 is still great platform and performs essentially identically to APM 2, so that might be a better choice for you if you want the hardware MUX.
That's going to be what we do for now. I was really looking forward to having the extra code space the MPU6000 frees up though. The other thing is that it looks like all the development going forward is for APM2 and that you won't continue to support APM1 much longer.
I've bought a good number of 3dr boards, and I haven't yet found one I can't use. I've even been buying up old boards on Buy, Sell, Trade.
Since the 1280 has become a pain with the current ArduPlane, ArduCopter, they still work great as trackers, and for too many projects to count - wireless sensor network controllers, ArduBoat/Rover, I'm using one as a controller for an RFID reader.
I have three APM1 units, and I love them, lots of great features. You do have to be careful when running quad software... I have two different RC RX cables, both custom made, one that has all eight connectors for ArduPlane, and one that has only 7, for 'copter.
Everything gets obsoleted in time, or we would not progress, right? As this is hobby-targeted gear, you can keep inventing new projects for the gear.... or for school or research, the original code that worked on that hardware still works, just branch for your purposes. That aide repeatability in teaching.
But in general, who would want their current gear to be good forever? As nice as it might be to feel secure in your "investment" it would also mean that you never advance... I think too many people think of APM1 and APM2 as being strictly generational, when in fact they both have unique advantages, and in some ways APM2 is more advanced, but in other ways, it evolved in terms of cost savings, and the APM1 is sort of the big brother in most respects... APM1 has a lot of features not found on APM2.
Anyway, my point is I have no worries about APM1. When ArduCopter or ArduPlane are no longer supported on it, I'll have the old code, and dozens of alternative projects to use them for.