Well if you have two complete spaceships you're just gonna end up with two different mission profiles. Though given how often they're the only ship in range... two smaller ships might be a good thing instead of one big one.
But to the saucer separation? Well... it seemed cool at first, but it just wasn't practical. Both from a budget and effects issue, an aesthetic issue as you mentioned, and a practicality issue in regards to the ship. How often do they have time to separate and how often would it seem that saucer is just vulnerable on the edge of a battle zone? Really the movie Generations gave it it's most practical use... a giant escape pod.