Miscellaneous/random comments:
1) CX operates a few routes within Asia that do not go through HKG-
SIN-CGK
SIN-BKK
TPE-NRT
TPE-SEL
2) In my experience, BKK-HKG-BKK is frequently half the cost of HKG-BKK-HKG. All other things being equal, BKK is usually the cheapest place to originate flights. Surprisingly, CGK doesn't offer any great deals on int'l fares.
3) In hitting multiple destinations economically, it may make sense to book roundtrips out of BKK with intermediate stops (i.e. BKK-HKG-MNL-SGN-BKK) that do not exceed the maximum permitted mileage rules.
4) In addition to its central location, BKK offers one of the best combinations of flight frequencies and destinations.
5) If you do decide to book a rt to BKK, you might be able to squeeze in one extra free (or virtually free) destination by actually making your finaly desination somewhere else in SE Asia w/ a stop in BKK. A good candidate for this extra stop would be somewhere that is not on the way to anywhere else you are planning on visiting-- for example, Chiang Mai, Chiang Rai or Phuket.
6) I travel to CGK frequently and have never had any problems. However, most people I know that either live there (including locals) or have frequent business there make it a point to monitor the situation closely. Infrequently, the highway between the city and the airport can be closed by disturbances.
7) With one minor exception that I'm aware of, Bali hasn't been affected by the turmoil that has impacted the rest of Indonesia.
8) With only 3-4 weeks, don't try to pack in too many destinations, or you won't really get much of a feel for anywhere, and will end up spending too much time on planes, going to and from the airports, etc.
9) Personal SE Asia favorites: BKK, PEN, DPS, SGN, Ko Samui, KUL, SIN, HKG.
10) BKK might be a good origination point for DPS packages. Most times of the year, TG has a daily non-stop flight from BKK to DPS.
11) With respect to security, I would avoid rural areas of the Philippines and Indonesia (Bali excepted) and some areas of Jakarta. Also, although I have felt personally safe along the Thai borders with Myanmar and Laos, skirmishes erupt periodically and there is a heavy military presence (checkpoints, sporadically closed roads, etc.).