“I wish Mastodon would stop building apps and focus purely on the protocol.”
Mastodon is a software. They don't work for the ActivityPub protocol.
The ActivityPub protocol is handled by the W3C. There is a W3C Working Group for ActivityPub, which interested developers can join and have a discussion, regardless if they are the developers of the Mastodon software, Hubzilla software, Pleroma, Misskey, etc.
So, yes and no. Yes, the Mastodon team is focusing on building apps because that's what they do. And, no, they cannot focus on developing the ActivityPub protocol because that is not under them.
Just clarifying so it's clearer. ^_^