I use nnmh for my mail backend.  In addition to missing sequences (and
not just unseen, by the way), I've made my own functions for replying
and forwarding that are more closely tied to mh-e.  Doing it my way
causes conflicts between the Gnus and mh-e window config stuff and is
most certainly inefficient so given the thread about memory usage I
don't recommend it for anyone else :-) What I get are the annotations
on messages I've replied to or forwarded and I get to use my preferred
replcomps, both of which are important to me.  I guess that since I
don't use XEmacs I don't have a problem with mhe being non-graphical,
but I certainly agree about the clunkiness.  It's the reason I started
using Gnus for reading mail in the first place.