I think that Frakes is a competent director, and I am sure that he would have done as good as job as he could with the material that he was given. However, it's hard to say what impact it would have had on the final product. Frakes did a good job with INS, but the script still had problems and the visual f/x work was largely mediocre (things that were likely beyond his control). We all know that there's a fair amount of deleted material from NEM that Stuart Baird cut in order to speed up the action. Some decent character moments were cut that Frakes may have kept in. Maybe Frakes would have cut down on the dune buggy sequence or trimmed other scenes, instead. It's hard to say exactly which material would have remained in his final cut. The actors' performances likely would have been influenced. Baird was not familiar with Trek or the actors, and there's been a lot of talk about issues between the director and the cast. Frakes probably could have gotten better results from the actors. Frakes also would have likely chosen his own crew to work on the film. We could have ended up with a different D.P., a different costume designer, etc. Frankly, despite all of the film's faults, I think that it "looked" really good so I can't bash Baird on that, at least.
So there are definitely things that could/would have been different with another director at the helm. However, despite all of this, the film's weakest element - the script - would still pose the same issues. We'd still have the Shinzon/clone story. We'd still have the Data/B-4 story. We'd still have the plot holes and the story would play out the same. It would just be wrapped in a different package.