I do not agree with the idea of joining of all sources, but surely a
   better dependency tree in the makefile that could make my new config
   compile without removing all compile tree would be nice.

There's already a start to this (that wasn't present in all ports until
a few days ago) -- the `links' target.  Basically, you do:

make links

in your kernel compile directory, and it looks for source files that
don't have any important #if's in them, and symlinks the object files
from ../GENERIC/foo.o to the current directory.

Unfortunately, there are so many scattered #if's right now that this
isn't very effective.  It would be cool if someone cleaned up a few 
of them.