It's interesting how the production method of an animated show—traditionally hand-drawn, Flash-style "paper" marionette, stop motion, or 3D CGI—can so deeply affect design. I've noticed some long-running shows switching from one to the other, typically from hand-drawn to Flash-style, and there is just something... off about them.
The majority of examples come from shows produced for public television, where budgets are more constrained, reliant as they are on endowments, grants and viewer donations, making the transition from more expensive hand-drawn methods toward the considerably cheaper Flash style understandable. All video links are to YouTube.
(Quick aside: one of the aims of my Lightbox animation software project is to narrow the expense gaps between these methods, by applying image processing, machine vision and even light artificial intelligence approaches to the animation production process. More on that some other time.)
Take Arthur, the PBS Kids TV series created by Marc Brown that revolves around the life and times of 8-year old anthropomorphic aardvark. Here's a random episode from season 5, and here's one from last year. (Skip ahead about 2 minutes, past the intro, which has been in use for years and was made using an earlier production method. So good, though!) It's subtle, indicating a tremendous level of skill applied, but you can notice little stiff shifts and stretchy "tweens" on characters that weren't there in the earlier episode. There's also a giveaway whenever a character turns its head 180 degrees, as the turning head is replaced with a different drawing facing forward, then another animated section to finish the rotation to the other side.
These are time-savers, but for someone familiar with the show from years ago and attuned to animation nuance, it's a clear decline in visual style and fidelity.
A much worse example is Caillou. Here's an early episode, and here's a more recent one. In the latter you can clearly see how appendages and even the heads take on a "paper puppet" visual character. (It doesn't help that the quality of the drawing is also much worse.)
This decline is not an intrinsic of "Flash-style" animation, but rather a consequence of linearly adapting a design prepared based on a different production method. As a counterpoint, Martha Speaks is an excellently designed show done in paper puppet fashion—and Word Girl a poorly designed and sloppily animated one, with tweens ev-er-y-where (but the writing is pretty clever).
I'm yet to see a show transition from a hand drawn design style to a puppet-and-tween-based vector production method without its visual presentation suffering for it, however slightly. In fact, this effect is so strong that even a completely new show, albeit based on the same source material and with an inevitable creative debt to its predecessor, can not seem to escape it: Bryan Redeagle (@misterpoppet on App.net and Ello) pointed out to me the 1994 to 1997 The Busy World of Richard Scarry and its decade-later sequel, 2007 to 2010's Busytown Mysteries (aka Hurray for Huckle).
At this point it is my thesis that it is an intrinsic, fundamental trait of any animation production that must be carefully considered up-front, and a part of the process that I'm now thinking about how to facilitate with digital tools.