As of more recently:

• The identity system is still the same, keys aren’t rotatable and still the core of your account. Outside of edge cases like Frost Bunkers (outsourcing key management to a cluster of third party servers), or platforms like DiVine letting you register with an email, keys remain pretty much the same.
• Private infomration like DMs have been altered. They’re still E2E encrypted, but now only the people involved in the conversation can request a copy of the encrypted DM (I assume that’s what you’re referring to, but I may be mistaken).
• Media attachements are usually uploaded to Blossom servers now. Standard notes still only embed remote media, but the ecosystem has a semi decentralized means of hosting content, and most clients will have a more standard ‘upload and share’ type of feature that most other platforms/protocols have.
• The more recent outbox model (on supported clients) allows you to set the relays that will host your content and replies/reactions to your content, diversifying the ecosystem away from a handful of big relays. Software like Ditto also provides a more Mastodon community style experience - even to the extent of supporting the Mastodon API.