well for one you should keep the site up 24/7 and fast as fast as it can be.
few other suggestions.
1-I dont know its just somekind of a dream for me to find everything in one site.Make a deal with the big traslators like IES,MRI alliance and others to release their manga's here too.May be official threat's.this way we can find releases with out looking every god damn scanlation site.Uploader team can re distrubute among other fileservers.(even dlcs(containers) or link directors can be argueable)One Big happy family.
2-A new front page that shows new releases in detail.And news.Like a portal.(this could be customized with tagging feature)
3-Personal Manga.I mean tagging specific manga (like i always read naruto and bleach) and when you login the new releases will be on your rss.
4-Working rss.(i dont know maybe i couldnt figured it out.)
5-This is more of a question than suggestion.Login is always a big problem to me.There should be a chance to keep logined till you log out.I use firefox and after few hours in the net i had to login again.
6-Bigger archive.I mean i couldnt find kimi ni todoke here.Which i think one of big mangas.With a deal with the release groups this is also not too hard.
7-Diffirent language's German french Russian spanish (this can be customizeable depending on user)
8-When i want to download a manga i had to go through few pages.There should be a way to reach the ddl's with one click.
Editheew.When i looked other posts there is like one or two suggestions.Didnt wanted to complain.Just i like this site very much.