I haven't gotten a single message from a Skype bot in over a year. Sure, Discord may not have too many yet, but just wait. When it becomes more profitable to allow the bots than to block them, Discord will have them too. The same thing has happened to every communication method in the history of man. When the carrier decides they either can make money off soulless selling machines or that it's simply not worth the money to keep playing 'cat-and-mouse' with them, they'll enter the playing field. And as to the 'bot ecosystem', good. I'd prefer a bot-hostile ecosystem, where every user account has to belong to a human being and every account online has to have a human behind it.
You're right, there are no channels in group chats - why would someone need a channel within a channel? If I want a group chat with a specific group of individuals, it's trivial to create one and add people from either another chat or my friends list. What you're asking for seems somewhat silly to me. I also don't understand what you mean about a 'separate community mechanism', the group chat is a subcommunity within the Skype community. If I want to contact someone, I just find them in my friends list and send them a message. They'll get it the next time they're online.
I'll agree with you, the permissions controls aren't there - the solution is: don't add people you don't trust to a group chat with people you care about. If you want permissions controls and bots galore, go to IRC.
I disagree about the notification system; I've got two groups set up that only pop up unread if my name is said. It's not a "mention" filter, it's a word filter which I typed my name and my nickname within the group into. I also don't care one iota about cross-device syncing, it's not my use-case. I have one computer. That's all I use when it comes to chatting. I don't use a device (i.e. anything that's not a PC) to do a great deal of Internet things.
Social engineering is going to happen no matter what the platform is; that's the whole point of it being social. Heck, the first 'hackers' were arguably social engineers. You can't really defend against it as a platform, all you can do is educate. I'll grant that Skype doesn't do that well, but neither does IRC or Slack.
Also, my computer is not from the last half-decade. It is an x86 machine with 1GB of RAM and will remain such for the foreseeable future. I am not planning on upgrading, ever, because I don't see anything on the market that looks to me like a clear upgrade with no downsides to the software and peripherals I wish to run.