I have taken a few buses in the Philippines, I find them crowded and most of the passengers brought their bags into the bus with them. So, the aisles are crammed with bags and suitcases, I guess no one trusts that a checked in bag will be there when they reach their destination. Buses had the A/C up full and they were cold. Have a long sleeve shirt or jacket available - no toilet on board so go to the toilet first and keep the fluids down. I can't tell you if this is typical of all buses. Buses that I was on as part of a tour were better though. Money talks!
The only commercial buses I used in the PI were the Rabbit Bus company and the Victory Liner bus company and only to Subic via Dau.
Here is a few links on Banaue that I found on Google. Looks like a long ride.
Why not just add a day or two to the Banaue trip instead of doing everything in one day.
There are some tours to Banaue that might be simpler to arrange and safer.
http://www.destination360.com/asia/philippines/banaue-rice-terraces.php (Sample link.)
I never thought of April as high season. To me high season is usually when it is cold in N. America and N. Europe which would be from around November through to March. If anything you would be at the end of a high season. December and January are definitely crowded because many of the Filipino workers come back to the PI for the holidays.
If your first foray into Asia was Thailand you will find the Philippines a little more expensive. If you were staying in a place in Thailand for the equivalent of $10 US you will find one in the Philippines too but the place will be more ratty or very basic (even with walls separating rooms made out of woven straw or reeds!) My preference is a private room with my own toilet, shared toilets usually are not the cleanest, but that is an old fart's opinion.
Be aware that most Seven Eleven stores, hotels, banks of course, malls, casinos and bars will have armed guards at the front door! Lots of private armed guards in front of many places. This is normal, been this way for the past 12 years. When I was in the Navy and visiting there I never noticed them 25 years ago though.
One benefit of the Philippines over other Asian countries is that almost everyone speaks English, signs are in English or Tagalog. You can use a dictionary with Tagalog if you want but English will do 90% of the time.
I usually stay in the Ermita area of Manila. There a few bars in this area that you can ignore - not the same as Bangkok though. Various priced hotels and a few hostels in this area. I have used the Stone House B&B on Mabini Street. Various priced rooms from dorm to private rooms with air (1000 P.) Fan only rooms are the cheapest. Easy walk to Robinson Mall, travel agencies, markets, restaurants even casinos. Mabini Pension is just down from the Stone House, avoid the fan rooms at street side - blinking sign will keep you up at night and jeepney road noise is loud. A/C room will be okay since you can shut the windows.