The user interface. I've always disliked SMF's user interface. I haven't used the script as an admin, so I have no idea what the admin panel looks like, but on all the SMF-based forums I have been, I've always found it difficult to get my way around, to find my posts, to edit my profile etc.
I have no idea about the admin interface, but the forums give me the impression that they are not very flexible. The themes most of the time seem pretty basic colour swaps. There are a few that are crafted with a lot more skills but I haven't seen a skin that radically changes the location of SMF elements like I've seen in MyBB and phpBB.
From the user side, it just feels like a really old software. reading the last 10 posts is a feature I used to like, as you can actually read snippets of the last post, instead of the thread title bumped, which will give me more curiosity and egg me to already draft in my head a reply. It works great for small activity forums but quickly becomes pretty messy as there is not a quick way to check out the threads that received activity like the conventional "New Posts" format most forum use.
If a thread receives 5 posts and another receive 2 in between. SMF will show me 7 posts, which I can read in reverse and get an idea of which ones relate to what discussion. In another community, I only get 2 thread titles in the results, but I have to open them to see what has been posted if it was new.
If SMF recent posts, bundled by thread those recent posts and had snippets that you can click to read the rest (like Xenforo quotes), I definitely would prefer this system as it would encourage discussion than just reading the thread title
If I click Profile it takes me to my Profile info instead of my Profile Editing page.
With all that said, they are not major gripes and I find myself easier in a SMF than a Zeta board.