I spent a month in the Philippines last winter. What are you interested in doing? The country is pretty varied and there's a shitload you can do and where you want to go depends entirely on what you want to be doing.
El Nido is extremely beautiful, although a bit out of the way - that's also a positive though because the amount of tourists is bearable compared to some other similar locations in SEA. A lot of jellyfish when I went there, although there's beaches without any as well. The town itself doesn't have any beach to speak of, rather it's surrounded by islands with plenty of them. Most people get tours for island hopping, which is fun, but almost all tours go the same few routes so it's not exactly peaceful. If you want peace, you can just rent a kayak and paddle to a random beach and have it pretty much all for yourself.
I'm not a huge fan of Cebu. It felt like a smaller version of Manila, ie. dirty and full of hookers, but I didn't go there for those. There's lots of malls where you can get anything you could ever want for cheap though. It's also the transport hub for the Visayas region, which is filled with smaller islands with pristine beaches and the best diving sites in the Philippines if you're into diving, so it's easy to get from Cebu to wherever you want.