Yeah, it's sad about the loss of Mr. Haney's voice actor. His voice was noticeably old-sounding in Season 16's "Get Smart." Miss Turner (the librarian)'s voice actress is also sounding pretty old nowadays, too.
However, compare Season 17 with Season 16. The animation is slightly improved: the lines aren't so thick anymore, and movements are more smooth. Honestly, I am glad 9 Story Entertainment took over, otherwise the show would've been canceled with Cookie Jar shutting down! (I believe DHX still owns the rights to the series, but has 9 Story produce the new episodes, like they do with "Johnny Test.")
A big advantage on the Flash production is that it allows them to do the animation work in-house, instead of subcontracting to a studio based in Korea or the Philippines or whatever. But not all Flash animation is bad: I've seen a few bits of Season 17 animation that was at least up to par with the episodes made at least five years ago. Plus, we have other shows with good Flash animation like "My Little Pony: Friendship is Magic" and "Foster's Home for Imaginary Friends."