I'm not familiar with WEG D6, but I recall from Saga Edition that there was a not-so-sweet spot for light transports in that system - large enough to be more easily targeted by capital ships, but small enough that starfighters are a significant threat. There was an option in that system to fit thrusters that would allow a transport ship to engage in dogfighting, which sounded cool but was very inadvisable in practice, as the ship's size and manoeuvrability worked against it in practically all the available dogfighting manoeuvers.
Likewise, in the X-Wing and TIE Fighter PC games, there was a size bracket at which craft would go from being targetable only from short range, like starfighters, to being easily targeted at medium range, and a lot of transports and shuttles ended up on the wrong side of it.
True enough, but it's a consequence of the genre to some extent. Even small squadrons of starfighters can be a major threat to capital ships, and hero ships tend to straddle the line between starfighter and gunship.
Well, they've got the Arquitens light cruiser and Gozanti transport. They're both a lot less intensive in personnel requirements, and we see them used routinely for patrol duties in Rebels.