The old town and surrounding area is interesting for the reasons stated above, but the resort area, like Pattaya is full of girlie bars which are a not the most attractive part of Thailand.
I hv only been to KL, Kuching, Miri, a long house and Tioman Island, which was fun. I went overland from Miri across jungle and by river to a long house, which was a wonderful trip. Someone I knew had connections, so it is not possible to replicate unless you get lucky. I travelled overland from Singapore to Tioman which is a good way to back pack. It is fairly inexpensive but maybe Thailand and Indonesia are cheaper. Try to get off the tourist trail.
What is best way to go? Fly direct or via HK and boat? what is best way to travel around in Taipei/Taiwan?