PH / Cebu resident for 9 months. I'm in Manila now and I miss Cebu already. Cebu is the best place to experience what Filipinos are known for - their warmth. Manila is just a city, lots of people in a rush, malls, and buildings. Nothing else much and does not compare to almost any other capital city in terms of stuff to see.
I've been doing 3-5 day trips to Siargao (surfing and Bali / hipster vibe), Leyte - raw and rugged waterfalls, beautiful hills, no foreigners, Siquijor - huge and beautiful waterfalls, and Bohol which I visit almost monthly - nice mix of party vibe, beach, and cool day trips.
There is no reason to go to Manila unless you have business there, friends to meet, or want to burn some Hyatt points (I'm at the GH and HR now).