I think the lack of hiding of previously viewed posts is one of my biggest gripes. I used to use Hide a lot in Reddit but all the alternatives are missing it.
A few other issues I have:
the need to click into threads to open a link is annoying
the inability to open comments and links in separate tabs/windows
lack of flair - /r/nfl flair were really nice, for example
I think the lack of hiding of previously viewed posts is one of my biggest gripes. I used to use Hide a lot in Reddit but all the alternatives are missing it.
A few other issues I have: