If I recall correctly there is a rule for Feddy starship design that says that there has to be an even number of Nacells. And to the best of my knowledge there has only been one exception, and that being the Enterprise from the end of TNG. Though there excuse was that canon wise that ship never really existed. There are some others, like the bridge having to be on top of the ship as opposed to buried deep inside of it like any sane person would do.
Well, the Freedom class is just as canon as the Cheyenne (which is already in this game) and the ship was included into the show at a time when Roddenberry was still alive so he obviously didn't veto the thing.
An interesting "excuse" I once read was that in TNG era ships the warpcoils in the nacelles were in pairs, therfore circumventing the odd numbers rule.
Oh and there were additional rules to Federation starship design:
*EDIT: Adarandrel beat me while I was typing*
The collectors of the warp engines have to be visible from the front and the nacelles need to have line of sight to ech other over at least 50% of their surface.
I think that's the "true" reason for the fold-thingy on the Intrepid, they wanted to oblige this rule.
Personally I think the Challenger, Freedom, and (to a lesser extent) the Niagara classes are some of the ugliest ships Star Trek has come up with.
That said, there are only so many ship classes to pull from the shows and movies, and these ship do have their fans. So I'm going to surprise even myself and admit that I support this idea. And hey, even though Star Trek only has one undisputed miracle worker, maybe Capt. Logan can create an alternate skin for these ships that would make them look good.