Well, playing around with the character skill creator. Since we get limited skillpoints it is obvious we can't, or shouldn't, just put skills wherever we want if we like to be somewhat effective at the end. This leads me to think of the two ship-classes before the last one.
Once you've escalated to the next rank, your previous ship is pretty much obsolete so why would you invest skillpoints there when you have a finite amount of it and rather want to use some for later on? (Somewhat rhetorical question)
Which again makes me wonder, what if one could make the smaller ship classes useful later on as well. Give them roles that can't be filled by their larger brethren. Make them more difficult to hit, faster, agile and so on? It would make fleet battles more interesting as well