Hello! 

My comments below:

Is there a way to separate chat messages with your chat on the right and others on the left?

Do you mean to make scheme of the messages in history area like in Whatsapp? By default it is not possible, but can be added as additional option.

Also will messenger be getting any chat bubbles? 

Sorry, I don't understand. By default it shows in Notifications - number of chats with new messages.

Last how do we get rid of military time and have regular time in the chats?

Which area with time do you mean?