Unless there's any practical reason, then in general we'd probably want to generate ELF executables. There's no pressing reason we particulaly need to stick to AIF, unless you have some tools that only work on them (say, !DDT: DeskDebug OTOH is getting ELF support).
I expect that adding AIF output to 'ld' wouldn't be especially hard, but it's extra effort. One of the things about ELF binaries is that the various tools also work on them as well as object files. This isn't the case for AIF.