First: Slackbot. This is a Slack-run bot that's in every channel; team owners can customize it to do various things, like scan messages for keywords and give out canned responses. Even if Slack adopted some variant of encrypted chat, each message would still need to be readable by Slackbot, so Slack would still have the means to collect every message.
Second: channel history. When I join a channel, I can see the messages in that channel from before I joined. This means that Slack (the server) must be able to give me those historical messages. In an encrypted group chat, the messages are encrypted only with the keys of the participants at that time, which means newcomers can't read them.
I'm sure there are other features in conflict with end-to-end encryption, too; these are just off the top of my head.