This is an endless topic and a popular view is that there's no way to properly represent brilliant pilots because star fighters are too much like eggshells. Anakin is one of the best pilots in the galaxy but the enemy fighter rolls well and hits, disabling Anakin's craft and leaving it floating there in Space. There are some talents that will help but (a) they're hard to come by and (b) don't really change things that much.
I have not thought this idea through so consider it a starting point.
In regular combat a defending character can make it harder to defeat them by piling on the Brawn / Soak. In Space combat there is no parallel to this so even great pilots can be brought low easily. You don't want to make ships unrealistically tough because (a) that doesn't fit what you're describing and (b) it's something that applies across the board rather than just the ace pilots. So I see two options: (1) allow someone to reduce damage based on their piloting skill somehow. (2) Make it harder to hit someone based on their piloting skill somehow.
Taking the second idea first, you could switch the difficulty for attacking another ship from just being based on their Silhouette difference, to being more like an opposed roll. So if you attack someone with Agility 2, it's 2 purples. Attack someone with Agility 2, Piloting 1, and it's 1 Purple, 1 Red. You could also modify it based on Silhouette. Upgrade or Downgrade once per difference in size according to direction.
Of course it gets rather horrifically high if you're targetting a really, really good pilot (so someone with 4 Agility and 4 Piloting would be 4 reds). That's the main problem as I see it. But I don't have experience of high level play, yet. If 4 reds isn't too high to be playable, we could go with that. If it is, you could perhaps determine things differently. E.g. use the existing Silhouette difficulties but just add upgrades based on one upgrade per rank of piloting skill. That way if you're shooting some Nemesis hotshot (Piloting 4) and the base difficulty was 2 Purple, it would end up as 3 Red. Still nasty, but better.
The other option would be something like a Parry for spaceships. Perhaps everyone should be able to spend a Strain point to add their Piloting ranks to Armour as an Incidental.
There are things about these ideas that I don't like - they are an exception to the rest of the combat system, they make a particular skill more valuable than other skills. However, the basic problem I am trying to solve is finding a way to translate Piloting skill into longevity for small ships. Thoughts on these ideas?