Nice question, because I've thought about it a lot!
Right now, the maneuvering thrusters are very powerful, and you could get away with no main engines at all. But the question isn't their power: it's the source of their power. The main engines burn only electricity, while the maneuvering thrusters burn spent reactor fuel and electricity.
The basic idea is that the main engines are a lot more efficient, not a lot more powerful... but the spent reactor fuel isn't exactly rare, so the maneuvering thrusters aren't prohibitively expensive.
I thought this was a pretty good tradeoff. I don't want the ships feeling too sluggish, but I don't want people to rely on maneuvering thrusters too much.