Each thruster/engine combination changes the feel of the ships as they move and some of them are just not very responsive, but I think that is a good thing and not a glitch.
In fact, there are some ships that are too maneuverable, making them hard to control.
I've got this one that I built with thrusters that make it turn so fast it's difficult to get it pointed in the right direction.
I tend to pick the maneuvering ability based on the needs of weapon-aim...and a certain amount of combat balance. A ship with a long-range projectile weapon versus a short-range beam weapon, for example, need entirely different ways of moving.
I've found that it's rather difficult to get a direct shot with a beam, so I usually try to get it pointed to make the target ship pass through it as it travels; such a ship needs to be able to go fast enough to catch its target, but doesn't need to turn super-quickly in order to get pointed correctly.
By contrast, the ship that can fire a projectile doesn't need to go quite so fast, but getting aimed properly requires a certain amount of precision, especially with a weapon like Charbroiled, which cannot fire as frequently as Dual Shot, and needs far more accuracy to make a hit.
One thing I have noticed, though, is that sometimes weapons-fire will pass right through a ship, almost as though geometry doesn't matter in the least...and each of those shots seems to be hitting the edge of the target.
Is there simply have a sphere of impact that's that same size for each vessel in that size-class, regardless of how it's been built? Just curious.