Depends what you want to see, mate.
'The islands' in Thailand covers both East and West coast, so don't expect to see them all in two weeks.
Same goes for Malaysia, there's so much to see that you can't possibly expect to see a great deal of it in less than 2 weeks.
Singapore can be 'done' by backpacking standards in a few days, though.
My advice? Choose either the Thai islands or Malaysia, and spend the bulk of your time there. I.e: head over to the East Coast Islands and spend some time there, then head back over and see the West Coast. This will be your 'typical backpacker' scene of boozing, girls, tuk tuks and boat rides.
Alternatively, head into Malaysia and see KL, the Perenthian Islands, Cameron Highlands, etc. This would be a bit more chilled out, and certainly wouldn't have the same levels of drunken debauchery that the Thai Islands promise.
As for travelling, if you want to fly, then fly. But don't be put off travelling through Southern Thailand, hundreds of backpackers do it every day. The trains are perfectly fine, in fact the sleeper trains are really comfortable. Depends what kind of an experience you want, and how tight your schedule is.
Do yourself a favour though, don't try and cram everything in to your last few weeks, do a few things properly rather than a lot of things quickly. |