Not sure how this relates to the OP's question (Which I find fairly confusing to be honest), but $() has an advantage in that it's better "nestable", for example consider:
Code:
$(ls | grep $(cat somefile))
There are conditions where `` will fail.
As for portability: $() has long since been a part of the POSIX standard. Writing shell scripts with `` for portability is like modifying your programs for Windows 95.