So: Why not embed the inode directly into the directory itself?
Check out the Usenix Proceedings from the January, 1997 conference;
there's an article about doing something very much like your idea.
While I was there, I toyed with trying to add a similar (although not
quite as ambitious as was described in their paper) to ext2fs. That is,
instead of eliminating the inode table altogether, put a copy of the
inode in the directory, but leave a forwarding pointer in the inode
table for programs like e2fsck and dump which need to scan the inode
table.
It's doable, but it runs into complicating factors; how to handle adding
and removing hard links is one of the bigger ones, which you've already
identified.
In either the simpler or the more ambitious case, it would require
non-trivial modifications to the ext2 filesystem, and in the latter
case, the filesystem format would be completely incompatible, so you
might as well call it a completely new filesystem (which is what the
people who wrote the Usenix paper did when they modified the UFS
filesystem).
- Ted