I don't think that home-made crypto in Telegram is a problem. As long as it cannot be easily broken, it is fine. The real problem is that it requires a phone number (read: your ID) to use it and tries to steal your contact list to its servers. Also, it keeps your messages on their servers forever.

A messenger that really cares about privacy would never require user to provide a phone number and would not keep decrypted messages on the server.