Planning and taking a trip to China on your own is perfectly feasible, especially as you've traveled independently in Asia already. I'm about to leave for China, Vietnam, and onward shortly and have done almost everything myself, my second such trip in China.

My m.o. is to study guide books and online resources and get a feel for what I might want to do and where. I suggest you do the same instead of consulting a travel agent who may have limited experience in the country and who also is not YOU. If you study it long enough a plan will emerge.

I also suggest you leave open spaces in your itinerary for places that will appear on the radar as you travel. And they will and then you'll have time for the deviations.

Two Chinese travel websites, C-trip and Elong, have been very useful to me for flights and urban hotels. They're the largest sites in China and affiliated with western travel sites. I suggest you explore them. Travel arrangements can also be left for a few days before traveling in China. In fact some trains may not be available for tickets until you're in the city where you'll leave from and cannot be bought anywhere else. There are also online train ticket agencies but I prefer buying them on arrival.

It seems to me that you're a perfect candidate for doing it yourself - some experience, a desire to go off the beaten path and unhappy with the idea of a cookie cutter tour. Be fearless and go forth!

Madame Perdu - thank you!

Mme Perdu: do you mind If I ask where you went on your first trip and where you will go on your second?

Enjoy Vietnam - but careful crossing the road in Hanoi! You will love it, I hope.

My first trip was all in Yunnan Province. I flew in to Kunming from Bangkok and came out by boat from Jinghong into Thailand on the Mekong River. After arrival a couple of days making arrangements in Kunming then to Dali by bus, on to Lijiang by bus, flew back to Kunming and on to Jinghong. Spent time around Jinghong which I enjoyed before finding a boat down the river. A month altogether.

This trip is also a month. I'm flying into Shanghai, overnight and out again immediately to Xiamen. I'll stay a week, tour around from Xiamen, see some Fujian tulou and tea gardens. Fly to Guilin and be picked up by my guesthouse to stay 2 weeks in the coutryside outside Yangshuo. A few days are open then to visit rice terraces and tea gardens in the vicinity of Guilin. Then to Nanning where I'll catch the overnight train to Hanoi.

This time I'll be on my own the entire time in China. Last time a friend was along but since I do the planning and booking it's all the same to me.

Generally speaking I prefer small cities, towns & villages as well as the countryside to big cities. As you can see there are no big cities on either trip. This holds true most places I go, not just China.

There are more experienced China travellers than I am but I seem to know enough to get the job done and have a nice time. Knowing what you want is, of course, half the battle.

China is a very big place and I think that you have too many places that are quite far apart. Unless you have 2-3 months, you need to make some choices.
Before getting into each place, just a note on MmePerdu's post. You can buy train tickets from anywhere in China. When buying in a city other than your departing point there is a minimal charge of 5RMB. Tickets go on sale online 12 days ahead and 10 days ahead when buying in person.
You are not specific as to when you are planning to go in the fall but definitely avoid the first week of October, the worst time to travel in China.
For a 15-day trip you need to limit yourself to about 4 places, maybe 5 if they are close by. Every time you move you lose most of the day. I can't imagine someone visiting China without visiting Beijing. It is the capital, full of history and has some of the most important tourist attractions in the country (Great Wall, Forbidden City, Temple of Heaven, etc.). Budget about 4 days, 3 would be rushed. The fast train between Beijing and Shanghai is the way to travel. Do not worry about last year's accident, China has a better record than most countries.
If you think that Tokyo is modern, wait until you see Shanghai. Usually two days are enough for Shanghai as such. Then you can do some trips to cities close by such as Hangzhou and Suzhou or a water town like Tongli. I am not a big fan of Hangzhou. Yes there is West lake but I have never been impressed by any city lake in China. If you want nature go to the countryside.
Then you can add one more thing to this list. Huangshan is not too far from Shanghai although it is not a short trip. The mountain is spectacular (google it) but it is better done with a tour or guide for some people.
LiJiiang and Yunnan province is nice but you do not have enough time. The Yangtze river cruise is a big waste of time. If you want scenery go to Yangshuo (flying into Guilin) is you can squeeze it. You probably need to delete Hangzhou and or Suzhou to make it. You need 3-4 days there.
Chengdu too far, no time. Pingyao, not that far to Beijing and can be combined with Xi'An. Both are old historical sites. But you need to choose among your many options.
Most of these places are well traveled and it is easy to plan your visit there. Check the websites mentioned by MmePerdu for flights. Not a bad place for hotels too but you should also take a look at wotif.com. For trains, some of these itineraries sell out quickly (not the short distance ones nor the Beijing-Shanghai route) and you may want ti use an agent. I can refer one to you if you choose train travel.

"Chinese Railways now have a central computer reservation system, so you can normally buy tickets for any route, not just ones starting at the station you're at. Though it's usually easier to get tickets for a train starting at the station you're at, rather than one starting somewhere else and calling at your station en route."
http://www.seat61.com/China.htm#How to buy tickets

JPDeM is right about the trains. This is, I believe, fairly new information and will be very useful for me too. Thanks.

Hi, traveller2007 -

From your post, I have the impression that you have done a fair amount of research on travel in China and have made some decisions about what YOU want to see and experience. Have you considered going solo and independently? It is very doable. A number of us have posted trip reports about our solo independent travels through China. If you haven't already seen these reports, it might be worth glancing at them. You can find mine by clicking on my name; also look for reports by thursdaysd, nywoman, ekscrunchy, iowaredhead, marija, and others. (Sorry to all of you who I'm neglecting to mention.)

Hope that helps!

You had mentioned Tibet so if you would like to see or experience a bit of Tibetan architect or culture then Lijiang and Zhongdian (Shangri La) will offer that. Beautiful mountain sceneries and Lijiang old town is one of my favorite city to stroll around.

IMO Beijing and Xi'an offer a lot of historical sites while Shanghai is very modern and feel a lot like Hong Kong.

Have you searched the trip reports on Fodors for China? Personally I've only written two reports but I have been to most of the major cities and you might find them useful.

Lijiang and Zhongdian: http://www.fodors.com/community/asia/wonderful-lijiang.cfm

Guilin and Yangzhou: http://www.fodors.com/community/asia/come-rain-come-shine-guilin-yangshuo-and-longsheng.cfm

My trip report on Lijiang had the old link to my pictures from there. If you are interested here's the proper link for Lijiang and Zhongdian

Lijiang: http://khun-pook.smugmug.com/Travel/Lijiang/3733848_rLtdRf#!i=214502137&k=pe9wo

Zhongdian only a few picts: http://khun-pook.smugmug.com/Travel/Shangri-La/3740053_T36RX2#!i=214737020&k=gqN7c

password is "Fodors"

@MmePerdu - yes this is in place since January this year. Note that you need to have your passport when you go buy tickets as tickets now have your name and passport number. This is to get scalpers out of business.
These agents are the cheapest that I know of. They are Australian expats living in Beijing: http://www.facebook.com/ChinaDiyTravel You get their email if you click on "about".

I knew about the passport but had not heard about the new computerized system. Much better. It had to happen. Again, many thanks, JPDeM.

I should add that with the centralized computerized system it is now also possible to buy tickets online 12 days ahead. This is extremely convenient but not so for tourists as the official website (www.12306.cn) is only in Chinese and requires a Chinese bank-issued card for payment. So when tickets go on sale at the station 10 days prior the tickets are often all gone already if it is a "hot route" or some holidays. Tickets will also sell out in hours when school end and begins, long weekends or some tour group happens to ride this route.