All of this may have changed in recent months, but this is usually the case...
1. Unless I am way wrong, which I am often am, the only option to Alor is on Wings Air through Kupang. Wings is part of the Lion Group. Batik is part of the same deal. You can count on them weighing your bags and charging accordingly. Be certain to buy accurate weight in advance. Paying on the spot will suck.
2. To make the only flight to Alor from Kupang, one must either take a 2:00 AM flight from Jakarta or fly the day before and spend the night in Kupang.
3. There is really only one flight a day out of Alor to Kupang. They sell two, but unless there is some weird need, they consolidate everything to one morning flight per day. Keep that in mind when booking connections from Kupang.
Alor is awesome, but the challenge of getting to and from is for sure a huge factor as to why it stays off the radar.