Biggest complain for me is that the Slack UI gives too much weight on the fact that someone has talked on a channel. This makes me feel like I should be reading that, even though it might not have anything to do with me. This creates a whack-a-mole situation where I end up constantly jumping between all channels so that I wont miss anything.
Another thing that I really liked on Flowdock was that discussions had separate threads. Especially on channels that weren't your main focus but instead you were invited to in order to discuss some specific thing you could follow just the discussion about that thing and everything else can be filtered away. This also makes it easy to know what any comment is about, since you can easily read the whole discussion thread without having to skim through the whole channel. This works great even if the messages have days or weeks between them. (Instead of having just the direct mention as a point of interest you end up following the thread that you were mentioned on and you might keep following it for longer time, even after the highlight is weeks old)
There was a major annoyance with Flowdock as well. At least when I was using it there wasn't a search that covered all channels. You had to either know what channel the thing you were searching on had happened or you had to one by one go through all channels and do a search on each one of them separately.
Main point here is that Slack fails to keep my attention on the things that are relevant to me and instead seems to suggest that everything is critical to me. This makes it feel like addiction instead of a tool that would be useful all the time.