Good CGI is expensive. And it requires just as much skill to program wire frames and texture. Sure, Max from Blue Tax and Ratatoing may be done on a budget of 5 bucks and a half eaten sandwich, but Green Lantern didn't lose a crapload of money for the effects being cheap. I'm sure that Thanos at the end of The Avengers cost a fortune just appearing for barely a minute. And of course, the unproduced episode of Powerpuff Girls that was unproduced due to the high cost of animating the entire thing in CGI. The entire thing has become demonized because of overuse, I agree. Especially when these shows make the switch and its noticeable.
Stop motion animation is HARD! It's extremely taxing and time consuming, and you so much as bump the table, you lose a day's work. I can see why they forced that upon Fireman Sam. But Thomas was just done to look flashy. I'm sure they have a relatively respectable budget and things go haywire with the models... but I can't see the CGI being that much less than train models with interchangeable faces and unmoving plasticine people. They made the switch to make it look more cartoony and animated, and that lost the charm as far as I'm concerned. It didn't matter that the mouths didn't move. They weren't supposed to. And they weren't supposed to have individual voices and voice actors. But then again, if you look at what they did with Thomas, that's a drop in the bucket.