I think it depends on which stories you’re reading. My boys love Thomas, too, and I would highly recommend this treasury of Thomas stories: http://www.amazon.com/Thomas-Engine-Collection-Friends-Railway/dp/0375834095/ref=pd_sim_b_1
The illustrations are wonderful, the vocabulary delightful, and the stories engaging. There is a complaint in one of the reviews that these are not Rev. Awdry’s original stories–that they have been edited (for instance, apparently Sir Topham Hatt used to be called the Fat Director and the freight cars were called trucks). Well…I can live with that.
Some of the Thomas books my boys have borrowed from the library really have been twaddle and some of them have come directly from these original stories, so you just have to see for yourself with each book.