It's got to execute the 68k gate, because it doesn't know what the code is doing. You can dynamically recompile it, but you've still got some lookups to do to find the native code. Or you can put some heuristics in to find a standard gate and shortcut it. It's not just old libraries that this would have to happen for if you want to be able to drop ppc libraries in and have them used by 68k software. It could be any library that has ever been written.
You can write libraries completely in C, I wouldn't like to say how often in occurred but you don't need assembler at all (just compiler support for regparm).
I am not familiar with this terminology so I really can't comment.
The next problem is that we're actually talking about x86 not PPC. So all of your code is going to have to do endian conversions. You either go the amithlon route, but then software that needs to write little endian values will end up doing two conversions. Or you spend the rest of time changing code to do the conversion where necessary. Or you try to come up with a new compiler patch that allows you to selectively have little or big endian variables.
The compiler suggestion is not realistic in my opinion, no one would seriously consider it. You could create abstractions (for example a library for x86 apps) on top of all this pretty easily.
Actually come to think of it what would be better is not another amiga operating system on x86 but something that feels like wine (but more stable) with 68k and ppc emulation. Having seamless integration between your native os apps and amiga apps would be ideal (integration with the filesystem, clipboard, windowing system (resize, minimize, maximize, etc), networking stack). That way you avoid many of the problem like drivers, hardware support having to implement core os components like filesystems etc...
Because of the amount of effort, still being limited to single processor and no memory protection, how horrible all the compromises would be to get it working on x86 it's not going to happen. I can't see developers flocking to an operating system that is crippled with that amount of backward compatibility. You can't even support x64.
See my previous comment, I think much of this is not relevant if you aren't building the entire OS.
The Amiga is not likely to ever become mainstream again. Nearly all of the software that will ever be written for the amiga operating system already has been written. This is a sad but true story.
That said the amiga has tons to unique software that is worth salvaging. What most people really need is a stable, highly compatible, well integrated, convenient and non-cumbersome (not like uae) way of running amiga applications in concert with their more recent applications.
ARM is probably a better choice if you want to avoid the endian issues, but then you have new problems like lack of decent hardware. Rasberry Pi is cheap, but it's also not very good. Even the more expensive boards are pretty poor in terms of expandability. 64bit is also coming to ARM, but you'll be shutting yourself off from that too.
Meh ARM seems like a good match to me seeing how PPC is starting to disappear quickly. At least for MorphOS