I mentioned Threema in another post and talked about how there is a lot to do with key exchange that can make such apps insecure. In reading more about Threema in their FAQ, it appears that the app servers can either facilitate the key exchange or it can be done in person via QR codes.
Key exchange is going to be that part of any end to end encryption system. iMessage most certainly holds the keys and are thus subject to court orders, it appears Threema doesn’t hold the keys.
That alone doesn’t make it secure, as they note that they must know who to send the message to. Even though those logs are being stored, there is nothing stopping someone from forcing them to log that data and turn it over (which is what PRISM tracks), but this is where their location comes into play, and I’m not sure the Swiss laws on this stuff.
At the end of the day you have to decide who you are trying to protect your data from.