He posed a very simple question to me: Which did you prefer?
A simple question indeed. With a very complicated answer. Here's the fruit of that discussion, with a few other categories thrown in. Remember, everyone's experiences are different, these is just my impressions, coupled with the aforementioned discussion.
Getting There and Around
Philippines. No question. Tickets from Beijing to Manila start at $75 round trip. Domestic flights on Cebu Pacific were under $100. Meanwhile, we spent $600 just getting to Bali from Beijing, plus pricier domestic flights. Both countries have ever-changing ferry and boat schedules, so no edge to either there. Honorable mention to Indonesia for having mopeds available everywhere. Jeepney's and trikes are pretty awesome though...
Philippines. Unless you speak Bahasa, there is a limit to how far off the beaten path you can wander in Indonesia, although really, a seasoned traveller can go just about anywhere in the world. Meanwhile, the majority of Filipinos speak excellent English along with the native Tagalog, which has familiar hints of Spanish as well. Traveling the Philippines is also a remedy for the over-touristed Thailand/Laos/Vietnam circuit which is all too common these days. I've heard the Philippines of today compared to the Thailand of 40 years ago, before it became too popular. Go now and go often, before it's too late.
Tossup. This is tough. Both countries offer exceptional value for accommodations on the beach, a bottle of beer, or a delicious meal. Get away from Bali or Boracay and you can easily stretch your money further than many other S.E. Asian options.
Indonesia. With hints of Thai cooking mixed in, Indonesia offers banana pancakes for breakfast, fried noodles or gado-gado for lunch, and tempeh curry or fresh fish for dinner. The Philippines' only entry in this category is Adobo Chicken with Garlic Rice, which is absolutely delicious, but one dish is, i believe, the opposite of variety. Still neither country is a match for Thailand, or even China for that matter.
Philippines. Not really a fair fight, since Filipinos are arguably the world's more welcoming people (Subic notwithstanding). Most everywhere i went (again, see Subic), i encountered the friendliest people to date. This is not to say Indonesians are unwelcoming, but i bet knowing a bit if Bahasa would open up doors that would otherwise be closed.
Indonesia. If ancient temples, tribes untouched by Western hands, and diversity are your thing, you can hardly do better than Indonesia. And if these aren't your things, they just might be after an extended visit. With 17,000 islands and almost 600 languages, there's no shortage of variety.
Indonesia. I was partial to the rocky landscapes, sky-piercing volcanoes, and beautiful architecture.
Another Tossup. It's really hard to beat Boracay, given that it is the perfect beach. However, just for sheer volume of beaches to choose from, not to mention the beautiful ones we found, Indonesia is definitely a strong contender.
Indonesia. I'm not an expert by any means, and i've only logged about 50 dives, but there's a reason why Komodo, Sulawesi, Sumatra, and the Banda Islands consistently rank among the best diving in the world. Having enjoyed a liveaboard in Komodo, i certainly know why: it's nothing short of incredible. Now, i haven't yet done Tubbataha or Apo reef, but the ten or so dives i did were no match for Komodo. The Coron Wreck Diving of northern Palawan does not disappoint, however.
Indonesia. I want everything in my house to be Indonesian. Or Tibetan. Please. Indonesia just does handicrafts exceptionally well. I didn't see anything in the Philippines worth buying.
Both countries are relatively cheap once you get there. Both have amazing beaches. Both have interesting people and cultures and have stunning landscapes.
For the traveller on a budget or with a short time frame, take the Philippines. It hasn't been overly touristed yet, they speak English, and it doesn't take much searching to find your own personal paradise. Cebu Pacific has dozens of flights from Manila to the furthest reaches of the country to meet anyone's needs. Plus, the cheap international flight options to Manila make the base investment cost low. I sound like a salesman.
However, if you are going for 3-6 months, are a seasoned traveller and want to take it slow and have an adventure, Indonesia is the place. Every island will have its own flavor and i hear you can pick up Bahasa in only a few weeks.
So to answer the original question, as long as flights are too cheap to ignore, i'll keep hitting the Philippines. But when i finally shove off for a multi-month excursion, you can bet i'll be spending a few months in Indonesia.
But really, i recommend doing both. Life is too short not to.