Having to run a .bat file prior to building isn't really nice, and not 
something I and some other people on IRC would like to see in ffmpeg.

Instead, it would be nice if configure/make would learn how to handle .cu 
files, converting them straight to an object-file.
My idea for this would be to teach the Makefiles about .cu files, and using a 
shell script as their compiler.
That script can then call nvcc and include the ptx2c functionality, and 
additionally also calls the designated C compiler, so for the build system it 
converts .cu to .o.

I wanted to fix the Makefiles but find it pretty complicated. Are there any 
pointers that could be useful as a start point.

Yeah, they are quite complex.
From how I understand it, it basically should boil down to adding something to common.mak like:

CU2C=..../compat/cuda/cu2c.sh

%.ptx.c: %.cu
        $(CU2C) $<

Then adding something.ptx.o to the OBJS list _should_ cause make to do the right thing. But I'm not a Makefile expert.
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