If you want to go to a city, instead of Manila check out Cebu City. It's a little smaller, more affordable, less crowded, and the taxi drivers don't try and rip you off. I stayed at a nice upscale-ish hotel called Marco Polo for less than $100/night. Bathrooms are fine, whether you are in the hotel, mall, restaurant, etc.
Then you can take a ferry to Bohol, which has some nice beaches and other landmarks like the Chocolate Hills. There I stayed at the Henann Hotel which is also very nice and affordable.
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