Scale as been one of my gripes since beta. Look at the size of a shuttle compares to a Defiant or Saber.
I'm not a computer programmer but is it a huge problem to alter the sizes slightly.
The scale for almost all the ships are actually pretty accurate. The shuttles are an exception because their size was deliberately made bigger so that when people are flying them, they can actually be seen easily and is a concession to STO being a game also.