I suppose, but is "skipping ships" really a bad thing? When money still mattered for me, I skipped plenty of ships, but I don't think my experience was diminished for that. Being unable to optionally "skip" a ship would have felt way more restricted.
I do think small ships should have dramatically better agility than they currently do, and they should have significantly more efficient thermals than ships that need larger power plants - it makes sense that a smaller-capacity power plant can be designed to be more thermally efficient. I think utility slots should be revisited, as a lot of small ships deserve more than they currently have.
Those changes alone could do a lot to give small ships areas in which they excel, especially if gameplay around stealth mechanics - smuggling, sneaking data off or on to megaships and installations, that sort of thing - is enhanced.
That sort of change takes the current small/medium ship imbalance - a small ship can do it, but a medium ship is better - and flips it around the other way. To me, that's automatically more interesting than arbitrary restriction, purely to make content for the purpose of excluding certain ships.