The Mylyn project is currently not very active, with no release for about 2 years for the "main" parts. It comes with a non-negligeable UI weight (a lot of extra view, popping-up by default, usually using not so standard design which makes them look alien...).
On the media I'm following, I don't see many users mentioning they use Mylyn; so either it's the kind of thing no-one talks about, or (and it's my favorite interpretation), Mylyn doesn't have a big user base.
Note that I'm talking about Mylyn tasks, contexts... Mylyn Docs/wikitext still seems popular according to Marketplace and is to be considered separately.
IMO, those reasons are enough to remove Mylyn by default from packages and let people who want it install it by themselves rather than pushing it to millions of users who seem to not use it.
I've prepared a patch removing explicit to Mylyn tasks/contexts features in all packages: https://git.eclipse.org/r/161423
. If you want your package to still include Mylyn, please just answer this message or on the Gerrit patch before I merge it ;)