That's not a problem inherent to that particular movie. It's one that plagues basically every sci-fi/space production in existence. I distinctly remember watching the TNG finale where they had the future segment where Riker's suped-up Enterprise D decloaks and comes up from below to blow holes in the Klingon ships with its big-ass superphaser cannon thingy. The fact that it didn't meet the ships nose-to nose like it was on the seas was mind-blowing.
The fact that they pointed out the trope in the movie doesn't even help, because immediately after pointing it out, the Enterprise is guilty of doing exactly the same thing (why did they need to rise up dramatically to loom over the Reliant before firing? Surely they could've just tipped the nose of the Enterprise up so that the weapons array was able to hit the other ship without its line-of-sight being obstructed by surrounding saucer section of the ship?)
Of course, pragmatically it's only because a) meeting on a plane makes the old-school pre-CGI practical effects a little easier to manage and shoot and b) For whatever reason people tend to liken capital ship space battles more to naval combat than aerial combat. So you get slow, lumbering 2-D planar combat instead of taking advantage of the fact that there's a Z-axis in space and no external gravity to fuss with.