On a good day, a bus from the centre of Tainan to downtown Taipei takes less than four and a half hours. The high-speed rail (HSR) takes one hour 43 minutes, and is never caught in traffic jams. However, the HSR station is about half an hour from central Tainan.
Taking the Tainan-Taipei bus costs between NTD220 (mid-week) and NTD360 (weekends). Unless you snag one of the hard-to-book "early bird" discounted tickets, the HSR journey will cost you NTD1,350, and that's only if you're travelling before October 8. After that date, HSR fares will rise by up to 9.6%. Long-distance bus travel in Taiwan can be a little slow sometimes, but it's always a real bargain. The most expensive bus ticket is nearly half the price of a conventional (TRA, not HSR) train ticket, and usually the bus is quicker.
Buses also have a non-price advantage over the HSR. When taking the bullet train, you've no choice but to get on or off at Taipei Main Railway Station. Most bus companies, by contrast, making a few stops before terminating at or near Taipei Main Station. Kuo-Kuang services, for instance, stop within walking distance of Dalongdong Baoan Temple and then again at Minquan West Road MRT Station before reaching Taipei Main Station - convenient if your hotel is in the city's northeast, or if you simply want to avoid the crowds and stairs at Taipei Main Station.