True, yes... then again, I'm not a massive fan of huge scaling differences.
All the shows (and some of the movies) are fraught with it, unfortunately. It's rather irritating.
Imagine trying to fight a tiny ship with the combat we have in STO while in a huge ship. Not only would trying to see it be difficult, but you'd also run into troubles such as fireing archs. What a headache. :\
I don't know that it would be terribly that much of a burden, if we're going to look at this logically. If you know that a small bee is buzzing around you in the STO universe, you don't need to be able to click on it. Tab target. Of course there's also the option of auto selecting what is attacking you. There's turrets, there's mines, and there's the tricobalt whammy.
(Edit to add: There's also shield FX. When your shield is being hit, you can see from which side the hit came. Even if you can't necessarily see it, be it line of sight issues from your current camera angle, size, or you're too busy looking at something else, you still have the option of knowing generally from whence the attack came.)
What I guess I'm getting at is that there is a dearth of options available to the user. A runabout or even a light scout vessel is not going to pose a challenge to any of the 'ships' in game.
However, having said that, I can understand the art department having issues with detail and scale. I'm just saying that we should stick to the real issues here (the art department being a good example). Scale has to give way (at least somewhat) to practicality. Though, I would argue that if they can give something reasonable and accurate dimensions, they should.
*nods a bit* And if these ships / shuttles were to scale they'd be all but impossible to see (or target in PvP).
Checking the Defiant against DS9 for example, then checking a Galaxy Class against DS9 and then comparing Galaxy Class ships against the Defiant (all in the series) will show differences. Scaling is sadly not always 100% in the Series.
We always do our best to make sure that at least in the game we have things as linear and consistent as possible. Sometimes that means we make a judgment call. (Watch the TNG Episode "Disaster" in French sometime. The rank of "Commander" is translated 3 different ways in that one episode. So we picked one out of the three that was used the most in the series.)
As for us not being Trek fans... well, you'll just have to believe that I have never seen as much Trek material in the cubicles in any office I worked in. And, yes, I'm counting my own toys.
Why would anyone click to target in PvP? If you're using keys to cycle targets, then it shouldn't be an issue.