I'm only starting to deal with AVL2016 myself -- it's a completely new platform for Glen & the gang and there are still a few issues they have to work out with it before it will be up to par with previous releases. This is why I still haven't deleted my "Diehard" install (still good for audio/midi).
I can say that with "Diehard" and the other previous Debian Squash AVLs Vanilla always compiled, installed and worked without a hitch. I never installed L2ork in AVL (I have a Ubuntu/KX Studio partition for that and I'm mostly into Vanilla anyway) but others on this forum had no trouble with it after replacing the jack module. Neither Pd version was affected by the absence of Pulse Audio.
As I see it, the options for AVL2016 and Pd are this right now:
--Vanilla: Now includes the deken extension finder as standard, so adding all the libraries you need from Extended is much easier. Problem so far: I tried both compilers in 2016 and still get failed graphics renderings (i.e. gui bangs show up as blank boxes etc). Automatic loading of the system font does not work and I can't fix the issue with any of the font startup flags. This causes tightly-spaced patches to get messed up. There is another Sid-based multimedia distro -- i/o linux -- that has the latest Vanilla release in the repos. On i/o linux the graphical errors are not present, but the font issues are the same. I have not yet tried installing that repo package to see if gives the same result on AVL 2016.
--L2ork: Options as described in my last post OR you could also try the new PurrData version that is replacing it soon. It's not quite ready yet, but close. It is possible that the graphics issues are related to the outdated GUI and since the point of PurrData is to replace this, it may be a way to get past those issues. There's posts on here with links to the RC4 PurrData test release, thou you may have to compile it as I don't see any pre-compiled versions for Sid.. There is still the issue of the jack dependencies.
Let me know how you make out as we are in the same boat at the moment.