The Sama Sama hotel at KUL is pretty good for a layover and a rest from flying - links directly to KLIA 1 via a buggy service. You might get a deal if flying Malaysian too. My wife is Malaysian, from Kuching on Borneo Island, and we've tried numerous tactics, but usually we stick with Oneworld on a single ticket to avoid the transfer to KLIA 2 and plug onwards the same day. Sometimes your bags don't make it when checked through on a tightish connection.

One thing worth mentioning is that if you're on separate tickets, chances are high you'll get MAS to check your bags through from Phuket to London, where Air Asia obviously won't. Saves a lot of faffing around.