Jack, I can see what you are saying but don't think it is as bad as you may imagine. There is no 'PERFECT' build for every type of ship, too many variables as in personal preference for weapons, armour, shields, self-preservation etc. What Commander A might consider be an ideal build for an FdL because he only does exploration would be vastly different to what Commander B thinks for his PvP exclusive FdL. I still think there will be enough variations scooting around the black to ensure you never know exactly what you will run into.
True, there's no one meta to rule them all. Mini-metas do seem to emerge occasionally, mostly in PVP, but normally as a result of a new weapon or modification being OP. And they soon get nerfed.
But for me it's less about what I might run into (I'm strictly PVE) and more about a given build having a hard limit. If I build two identically specced exploration Anacondas (or give my build details to a friend) then given enough modification rolls both ships will be absolutely identical in performance. Gone is that subtle variation that might lead to one ship running slightly cooler, or another having an edge-case lower class OP power plant that doesn't require the hangar to be disabled while the thrusters are active. I never really went out of my way to seek out these things, but it was interesting when they popped out of the RNG and they gave the ships a certain unique character.
(Had we ever -- longest of long-shots -- been given the ability to trade modules or entire ships between players, these little details are the sort of thing that might have led to a interesting second-user ship market. "She may not look like much but she's got it where it counts, kid.")
Meh, it's not the end of the world. It's a very minor consideration within a system that's much better than the original IMO. We still have a bit of RNG on the level climbing, for those who get a kick out of "winning" a "lucky" modification that maxes out at four instead of six rolls. And I bloody love the ability to drive around on planetary surfaces, or drop into USS, and collect absolutely everything that's there without having to worry about material capacity. The magical bag of holding still makes no logical sense but the freedom of having a per-material limit instead of a global cap cannot be understated.