You raise an interesting point about effort. Discovery 'matchmaking' does not exist, it is as if in DotA all kinds of players from 1k MMR and 8k MMR are thrown together. Practice is everything in competitive games, and I will fully agree with anyone saying that if practice makes you better, you should come out on top. The problem is that neither Freelancer itself nor Discovery are really designed to be competitive like that.
And with that comes another problem that I believe to be another big reason for the popularity of capital ships amongst newer players: You can have the same impact and fun all of the skilled snub-enthusiasts have without having to put effort into practice.
Then again, it all comes down to what you define as winning and what you consider fun. If you getting a blue message is what you define as 'winning' and 'fun' and the point of Discovery then you are missing out on a lot, anyway.