There is nothing stopping a huge city-size ship from being as nimble and fast as a shuttle sized ship in the absence of friction. The contrary would actually be the case; the large ship with the larger engines would travel faster than the "fighter" with fighter sized engines.
That's reasonable insofar as it goes, but there are some subtleties to be aware of:
- Acceleration is a function of thrust divided by mass. A fighter tends to have a huge proportion of it's mass devoted to engines - it's doubtful that a city-sized spaceship would devote 50% of it's mass to engines - thus the fighter may still be faster.
- Even without friction, we still have inertia. The larger ship may be able to accelerate faster, but changing direction is going to take just as long.
- A trained fighter pilot can survive about 5 g sustained acceleration. It's doubtful that a city-sized spaceship would have the structural integrity to survive 5 g acceleration - and the humans inside would likely be pulverised by manoeuvres at those types of acceleration.