When comparing Messenger vs SecureChat, the Slant community recommends SecureChat for most people. In the question“What is the best team chat software?” SecureChat is ranked 22nd while Messenger is ranked 74th. The most important reason people chose SecureChat is:
Supports threads to organise conversations into topics.
Specs
Ranked in these QuestionsQuestion Ranking
Pros

Pro Uses Facebook friends to create a contacts list
Allows communicating with anyone who's a friend on Facebook.
Pro Read receipts
Can see who has seen each message in group messages.
Pro Easy to share posts from Facebook
Integration with Facebook makes it easy to share any interesting posts from the Facebook timeline.
Pro Great UI
User interface of the application is clean, intuitive and easy to overview.
Pro Threads to organize conversations
Supports threads to organise conversations into topics.
Pro Expiring messages
Channels can be configured to have expiring messages that get automatically deleted after a pre-defined time.
Pro Guaranteed delete
Ensures messages are fully deleted and removed from backup.
Pro Servers 100% hosted in Switzerland
Protected by Swiss data privacy - some of the highest data privacy laws in the world.
Pro Encryption
Strong end-to-end encryption of messages and files.
Pro Drag and drop files
Drag and drop documents, photos, videos into the chat.
Pro Integrates with other tools
Built in integrations for Zendesk, Trello, Github, SupportBee, etc.
Cons
Con Lack of privacy
Messenger is owned by Facebook. Based on their privacy policy, this means that any information you provide (including messages sent) are used by Facebook to profile you and sell access to your data to advertisers.
Con Lack of end-to-end encryption
Secret (end-to-end encrypted) chats are only supported in one-to-one messages, and are not enabled by default, and the encryption has not been verified independently.

Con Non-free / Propritary Software
The code base isn't free/libre and cannot be self-hosted, therefore there is no proof that encryption or "guaranteed delete", actually work. There is no reason to think this application is secure.
