In 2008, I did 3 countries, 8 cities, in 17 days, and I felt that was too much traveling. Seems like when we got comfortable in a city, it was time to hop the train again. I was in a similar situation @tinyfaery, where I wanted to see as much as I could because I didn’t know when I’d ever get the chance to go back again. I have little regrets, but there were cities and place I wish I had had a day or two more in, though that’s inevitable anytime I travel.
Seems that you have some of your priorities set, which is perfect. With the limited time and the distances between the cities, I think it’s important to decide whether you want to see just the cities, or both the cities and the countryside as well. Our main destinations were the major cities, but I was also interested in seeing the coutryside, especially Bavaria, so I was grateful we took the trains, despite the time some of those rides consumed. I remember looking out the train window wishing I could get out and go camping, or walk though the forests, etc., so even the train left me feeling I missed a lot. It was a great compromise in general, but when we did fly from Munich to Milan, it was quite depressing seeing the Alps from a plane window instead of being immersed in them.
I personally didn’t use a travel agent, and everything was pretty easy to do ourselves. The transportation specifically was easy to book here well in advance. Hotels and B&Bs are a different story, and all you can do is look for places in areas you want to be in, then just trust the online reviews and photos…yes you will end up with a not-so-great place to stay occasionally, but if it’s more about seeing the country and city, a bad hotel for a night or two will not matter much. I don’t think you need and agent, seems like a waste of money and I love DIY, but if you want to alleviate some stress from you life leading up to the trip, then it might make sense for you.
I also agree with @andrew, If you can keep a country, or specifically a city as a base as stated, I think that makes the most sense. I did this with Germany (well admittedly because I wanted to drink the beer! Mmm, beer!), and it was perfect…though we didn’t stick to a city, but instead did a loop and flew into Berlin and out Cologne.
Hopefully some of this is helpful! Good luck and have fun…even the planning is fun and exciting IMO!