In certain situations, tours are an excellent way to travel, either if you don't feel safe or confident on your own, or if you're travelling at a busy time of year an options for independent travellers isn't as good as those in a group. It's easy to say that it's a waste of time taking a tour, but everyone needs to start somewhere.
I've travelled with Gap in Cuba (peak holiday season, and didn't have time to organise an independent trip) and Intrepid in Vietnam (was only 18, and didn't know where to start!). I thought the Gap tour was awful (badly organised, poorly run), and Intrepid was excellent.
Having said that, I used to run tours for Imtrav in China, and got to know a lot of other leaders from other companies working in other countries....I think to be honest its really down to the local operations and your guide. Gap in Cuba sucked, but I believe they ware excellent in South America. Imtrav specialised in Egypt, etc. Check out which company started their life in S.E.Asia, and go with them.
Having said that, you are travelling for a long time, and I think you might get fed up with a long tour after a few weeks. I'd advise starting with the "hardest" country, and do that on a tour. By the end of your tour, you'll have built up confidence, and know how things work. You'll then be able to do the easier countries more efficiently and more cheaply.
In 2003 my sister and I booked a Beijing-Hong Kong tour. It was cancelled due to SARS, so we ended up doing the trip ourselves. It was hard work (not speaking Chinese), but we ended up staying in much nicer hotels, flying, AND saved money over the tour price.