Staying in Ajmer might be a good option as it's only 11km away from Pushkar. You might be able to hire a car or rickshaw to ferry you around while you're there. Rickshaw hire can be very very cheap, especially if you strike up a deal with an honest rickshaw-wallah, book him for a few days and all. It'll be a deal that's beneficial to both of you as you get your transport as and when you want and at a good rate, while he gets steady work at a better rate than he can charge locals.
I have heard very good things about Ajmer. Being a holy site for Muslims in India, it will provide you with a good picture of Rajasthan, especially when compared to Pushkar, which is holy for the Hindus. But if you are able to find a good deal in Pushkar, then you may be missing out on the atmosphere of the camel fair if you decide to stay in Ajmer (though that's up to you).
Train travel in India is infinitely more comfortable than bus travel, especially in Rajasthan (which has one of the worst bus systems in India, IMHO). From Delhi to Ajmer, Jodhpur, etc, train connections will be plentiful and fast, though you'll probably get on a bus at some point. I think bus travel in November will be much better (I was there in April at the height of the Rajasthani summer.. 48 degrees.. NO AIRCON).
If you're going to Jodhpur, I can happily recommend
Durag Niwas. The hotel was cheap, fantastic, and the host was great — he can point you out to the best places in town. I wrote
very briefly about Rajasthan, including Jaisalmer and Jodhpur, so you may be interested in taking a look.
On your way back from Rajasthan, you could perhaps drop off at Agra, see the Taj Mahal, and catch the fast train back to Delhi the same day. Agra can be done in half a day, so why not see the Taj while you're there.