If you're looking for a product built by top MIT engineers who spent years thinking about how to make chat actually productive, check out Zulip. I'm one of those MIT engineers, and I agree that Slack is a huge waste of time, for precisely the reasons you describe (here's our attempt at explaining how Slack wastes your time: https://zulipchat.com/why-zulip/, and how Zulip solves those problems; there's more on our homepage).
The fact that Slack is, in most organizations, either very low-traffic or a waste of time is why we don't market Zulip primarily as "open source Slack" -- it really is a different product, designed to be amazing for a large, distributed team doing a lot of communication, without things becoming overwhelming.
If you don't believe me, read this awesome cartoon by one of our users: https://twitter.com/b0rk/status/986444234365521920
(As another reason for Slack's success, I'll also add that a lot of "Slack clone" products are pretty buggy; everyone underestimates how much work a high-quality chat experience is. Check out https://zulip.readthedocs.io/en/latest/subsystems/markdown.h... and https://zulip.readthedocs.io/en/latest/subsystems/events-sys... if you want to learn about the complexity of a few of the more interesting challenges.)