I probably wouldn't count on PR joining an alliance anytime soon though I think that's too bad. They're really not a half bad airline, I've been on worse. Terminal 2 in Manila isn't too bad though Manila is hardly an ideal place to transit at least T2 makes it as pleasant as possible. The Philippines is so messed up in general that using any airport there is just pure hell.

You can get to a few places in the Philippines on miles from any of the major alliances, MNL and CEB being the most common. From there internal flights are VERY VERY cheap. Cebu Pacific tends to be the cheapest but I don't care for them. PR isn't much more expensive. These inter-island flights are really short and coach is quite survivable. I'd expect coach fares to run about $40-60 each way and Business class fares are $100-140 or so each way. On coach fares the Philippine taxes will be more than your actual air fare, I find it to be pretty annoying as they run a lot of super cheap fare specials but you can't avoid the $25 or $30 in taxes.

If you come in on any airline other than PR then you'll arrive at T1 (probably) or T3 (few airlines using it yet). T1 is beyond terrible and transiting from there to T2 for a PR flight isn't exactly straightforward. If you use Cebu Pacific then you'll be going to T3 but again they've made absolutely no logical way to transfer between terminals at this airport. If you can get an award ticket directly to Cebu then you'll find transfers much easier as they only have 1 terminal. I know KE and OZ fly to Cebu so that gives you at least 1 Skyteam and *A option.