I'll be going Japan in Dec and will be travelling fr tokyo to kyoto & back but do not want to take shinkansen as it's expensive. Any recommendation for overnight bus or train (seishun 18 kippu)? I've searched through the japan-guide.com website but the info is very limited.I'd recommend overnight buses which are cheap and convenient as you don't lose sightseeing time and save money on accomodation as well. The Tokyo-Kyoto route is highly competitive so the rates are low and start around 5000 yen. Here's one company that has english internet booking:
http://willerexpress.com/
If you are going for just a short trip from Tokyo I'd also consider JTB's Free Plan Kyoto 2 Day package that includes shinkansen and hotel for less than 20,000 yen.
http://www.japanican.com/tours/tourdetail.aspx?tc=GMT01TYOOVJH2KAK&aff...
For seishun 18 kippu, is it a direct train to kyoto or need to transfer trains?
While Seishun 18 Kippu is attractive because it is the cheapest method, it isn't very convenient and, if done by night train, takes about 10.5 hours and requires at least 3 transfers (the longest leg is about 7 hours long). If you travel during the day it can take about 9 hours and require at least 5 transfers. Its not a very restful trip and I wouldn't recommend it unless you are very fond of commuter trains.