I'll second that thought...
All my newer sites are extensionless and I'd remove 'em from the older ones, but I remember reading about how cool urls don't change (once upon a time, in a far far away place) and I don't want to take the 'transfer time' hit in traffic, otherwise I would.
IMO it's easiest, most consistent, and probably safest to just make the 'directory' (URL with a trailing /) a 'page' in the next level up, since directory1/directory2/ is really just an alias for the page /directory1/directory2/index.html (or whatever you may have changed your indexes to).
So, where you might save and upload index.html to /directory1/directory2/, I would change the name of index.html to directory2.html, upload it to directory1, then strip the trailing / and index.html from the URL if either was ever requested, which means I don't ever have to worry about 'duplicate content' at /directory1/directory2/ and /directory1/directory2/index.html, because they're both (easily) redirected to /directory1/directory2 (no index, no trailing /) and served the information from /directory1/directory2.html, which seems to make sense...
If you have a full directory of pages within a directory, I would think you could (should?) have a page that talks about the topic of the sub-directory in the directory and if you could not, the sub-directory probably doesn't belong where it is.
Stripping all the trailing /s and index.ext requests from URLs really simplifies the matter of going extensionless and leaves you with:
('index' for /dir/)
('index' for /dir2/)
You don't really need it if you do the preceding, but I always run with Options -indexes in my .htaccess as a 'backup' for the redirects.
In thinking about it, I actually can't remember using a directory (/directory/) as a URL in years, even with extensions? hmmm... I really can't remember the last time I did... It's been at least 3 years, maybe longer.
I often only have one index.ext on a site, which is what you get at the root, and happens to make it easy to not accidentally upload an index.ext to a directory it doesn't belong in... (Been there, done that, and it might have been one of the reasons I switched.)