We have just returned from Bali, we went from Newcastle to Jakarta via Dubai with Emirates, then used Air Asia for Jakarta to Bali.
Air Asia were ok, we booked a Jak-Bali flight for about 3 hours after our flight was due to land with Emirates and it was on time and fine, only about a third full.
For the homewardbound leg though, I would really reccomend you give PLENTY of time if you are connecting to an international flight. We actually booked the last flight back to Jakarta on the night before the Emirates flight, and stopped over in the Sheraton Bandera near to the airport. Even then, the flight was reschduled back 2 hours back after we had booked, and we had a further 3 hour delay on the night of the flight, so you can see why you need to be cautious.
However despite this, for the money the flights were great, and if you build in an overnight on your return leg, you should be fine.
Also, Emirates are well worth looking into as they were excellent, and fly from a number of regional UK airports at reasonable prices, which lets you avoid Heathrow.