I'm pretty sure Bruce Timm didn't do designs for this OVA... He hasn't been a primary character designer since Superman: Doomsday. That film had his fingers all over the designs (unfortunately) and was one case where they should have just re-used the Justice League/Superman:TAS designs but didn't.
There are several reasons why the OVAs don't look like the animated series. One is that each film is set in its own continuity and is not meant to connect to the shows -- they're their own entities. Why some fans don't understand this (or choose not to) I don't know -- I thought the film producers were fairly clear on this.
Another reason for the design changes is that after nearly 20 years people get tired of only one house style and it makes sense to do something different. Teen Titans and Legion of Superheroes as well as The Batman sure didn't look like Batman, Superman:TAS, or Justice League. Likewise, Batman: The Brave and the Bold -- which I think is the most succesful series visually this side of Batman: TAS -- is a very different looking series which deliberately emulates character designs and drawing styles from the late 1940s through the early 1970s eras of DC Comic.
Some people will never be happy if a show doesn't look like it was designed by Artist X, Y, Z. The main thing is if the film overall was a good experience.
Public Enemies was still a well-produced film. The vocal performances were great and overall it didn't look shabby, either. They tried their best to emulate Ed McGuinness style and came up with a decent hybridized animated variant on his pencils. It's in the eye of the individual beholder whether they were that successful or not.
I reread the original hardcover reprint of Public Enemies over the weekend and frankly was surprised by how little was changed for the film.