Is there an alternative to Messages?
The whole iMessage system is entirely proprietary, and there are no 3rd party clients available to use instead of the official ones, on either iOS or OSX.  That's not to say it won't be reverse engineered in time, but I suspect that Apple will fix any issues way before anything like that happens.

I too get messages that appear out of order and occasionally ones that simply never show on one device or another, but anecdotally I only ever see this when devices are playing "catch up" with messages that I have already read elsewhere.