It is absolutely worth remembering that flash animation is almost always a matter of budget. It's not like doing pre-production for the show, they had the choice between using motion tweens or getting Miyazaki to personally draw all 29.97 frames per second.
The difference between a typical flash animated show and say... the new Thundercats animated by Madhouse is probably in the range of at least a million dollars per episode. If the choice is between flash animation and something animated overseas that moves like a 70s Hanna Babara cartoon, it certainly has its place in the industry, or at least until the next cost-saving measure has its own particular aesthetic that's hard to avoid.
Studio B does amazing work with flash and the designs support that style. The fact that Lauren Faust gets a credit as executive producer is for the betterment of low-budget, north-American produced commercial animation.
(I say all this as a tv flash animator myself, so I lack objectivity and this is probably boring to everyone else)