I faced your issue as I sought to implement groupchats for my chatting app. I faced the same problem of MUC not storing offline messages for each recipient. And I did not want to retrieve MUC history which requires the user to rejoin every MUC to update his messages database. What I wanted is for the server to save offline messages by recipient, and for the recipient to get all MUC messages when he gets online (without having to join each MUC).
The way I did it is through pubsub. Using pubsub will force the server to store offline message per recipient. When the user reconnects, he gets all the offline messages including the pubsub messages which are sent as normal messages - that is it. One issue I had with pubsub over MUC though is that it is hard to get the list of subscribers. So when my app creates a groupchat, it creates a pubsub node for messages, invite all participants to subscribe (including self) to the pubsub and my app also creates a MUC and makes every participant an owner of that MUC. This way the list of the groupchat participants can be retrieved by checking the list of owners of the MUC. The only purposes of the MUC are to hold the list of participants as well as the name of the groupchat. Everything else is handled by the pubsub node.
Anything unclear please let me know.
ADDITIONAL DETAILS:
Essentially when the user wants to create a groupchat, our app creates a pubsub node as well as a MUC. You need to be familiar with both concepts. For the pubsub node, you need to set an option to allow any subscriber to post. When a user sends a message, he actually publishes on the node, and ejabberd will send the message to all subscribers as if it were a regular message (except it comes from pubsub.yourdomain.com). Therefore if a recipient is offline, ejabberd will store this message as any other regular message.
This is not how ejabberd handles MUC messages. Those are only sent to people CURRENTLY in the chatroom. History of messages can be stored by ejabberd however, but for a recipient to get the history he will need to join the MUC. Which means that everytime the app reconnects, it would have to join all the user's existing MUCs. We found this was not practical.
We also use a MUC for the same groupchat, but this is only to store participants so that a user can get the list at any time (no way to do it with pubsub).
An additional benefit of using pubsub over MUC is that the way ejabberd stores pubsub data is way more efficient. I have not studied this in depth, but I expect much better performance from pubsub.