Both offer beautiful natural scenery, but I am not the biggest fan of either.
Thailand is very developed and "first world." There is plenty of tourist infrastructure, but the downside is that you can feel very shuffled through as part of the crowd by a jaded tourist industry. (And I recognize that when I see it, as I lived in Hawai'i for several years.) Despite its marketing nickname "the land of smiles," in my experience on several trips the local people were generally not very friendly to tourists. The food can be delicious if you avoid the places catering to German tourists and serving weiner schnitzel.
Much of the Phillippines is desperately poor and crowded. People are friendly, but can be out to separate you from every dollar you have. A while back we went to Camiguin Island, which at the time was being touted as an up and coming tourist destination. It took us days of planes, trains and automobiles to get there. When we arrived folks were amazed to see American tourists - the only Americans they knew were their Peace Corps volunteers. The only other Western tourist on the island was an older guy shacked up with his local teenaged girlfriend. The folks at the hotel kept trying to set us up with "a couple of nice girls from Bohol," i.e., hookers. Until they figured out we were a gay couple, at which point they sent a hot young local dude sniffing around for opportunities. (Not that there isn't also a sex industry in Thailand, but I found it easier to avoid.) Also, I am not a fan of Filipino food.
Assuming you want to limit yourself to Southeast Asia, I personally have preferred trips to Laos, Cambodia and Indonesia to Thailand and the Phillippines.