I suspect that the puzzlement regarding the larger ships emerges from a collision between two sets of expectations:
1. You learn how to fly in a small ship. You then get progressively larger ships, but you never need to learn (and are never told) anything new about flying them -- the ship just gets slower. [I'm fully aware that we're only just seeing v1.1 of the prototype, and that there's a lot of hand-holding stuff that hasn't even been imagined yet much less implemented. I'm not criticizing; I'm pointing out how things appear at the moment.]
2. At some point in the progression from one-man fighter to corvette to destroyer, these names for size classes of ships imply that they eventually become big enough to require crews and officers... but we're still flying them as though they're one-man fighters.
A good case can be made for fighters and bombers to feel like nimble one-seaters. It makes sense that when you point one of these ships in a particular direction, that's where you can fire, and you're agile enough to be able to bring all your few weapons to bear by changing your ship's heading.
The "problem" is that (at least until turret control in the v1.1 prototype) as our ships get bigger and slower (which is not unreasonable), we're still expected to control them as though they were fighters... but they no longer behave like fighters. It's that clash of expectations that, I think, is making people go, "huh?"
I think there's a way to address this confusion and at the same time provide a blueprint for expanding Limit Theory to be more fun for more people. Put simply: anything bigger than a bomber requires crew, which implies that "the game" begins to change at that point to include crew management requirements/features. And the biggest ships would have significant impacts on the game world (with functional gameplay effects) just by their presence.
To begin with, you shouldn't be driving a capital ship by yourself as though it was a painfully sluggish fighter. You should be leveling up your crew and issuing orders from your CIC to manage information and direct operations.
And the bigger ship you get, the less tactical and more strategic gameplay should become. Choosing to move up to a battleship would mean choosing to give up seat-of-your-pants, adrenaline-pumping dogfighting in favor of more thoughtful strategic play that rewards careful planning and effective management of systems and people.
The flip side of this is that there need to be full advancement paths for all ship types. Because the tactical gameplay in a fighter is so different from the strategic play of a cruiser or carrier, these will (assuming "tactical" and "strategic" play are implemented differently and properly) attract different kinds of gamers.
Let people who like the visceral, kinesthetic experience of fighter combat get really good at flying fighters and bombers. They won't have as much cargo space so they can't do as much trading or exploring as someone with a corvette or larger ship, and they won't be as diplomatically imposing as a ship of the line, but these players probably won't be interested in that kind of gameplay, anyway.
Let corvettes and frigates and destroyers be about managing small crews with an emphasis on operations (rather than tactics or strategy): running mid-level missions, enjoying a balance between combat capability and trade/diplomacy, and generally being well-suited for exploration gameplay.
Finally, let cruisers and battleships and carriers be about strategic force projection. There shouldn't be many of these babies, but the presence of one (or the mere threat of the presence of one) in an area should modify local behaviors. A carrier battle group should dominate entire star sectors, affecting military activities, encouraging diplomacy, and defending peaceful commerce. Of course it should occasionally be necessary to bring the hammer down on miscreants, because, you know, what's the point of having that much firepower in a game if you never get to use it?

In each of these three general groups, players should be able to become recognized masters. If you want to stay a fighter jock, you should be able to do so, with increasingly difficult but satisfying content for fighter craft. Eventually you should be recognizable as a legendary fighter ace.
The same principle would apply to players who prefer the operational or strategic levels of play and skippering the ships that go with those styles of play. No one should have to stop playing the kind of tactical or operational game they enjoy simply because "winning" requires moving to ever-bigger ships with less direct control.
...
I recognize that this is a very different game design than what's visible right now. But I think it's a design path that makes sense. It builds on Limit Theory as it is now, and opens it up to people who enjoy different kinds of play without leaving behind those who like the kind of fast-paced combat play suggested in the current LT prototype.
If this seems reasonable, how could it be improved? If this seems wrong, what different design path would you suggest that achieves the same (or better) goals of building on existing LT while supporting other playstyle preferences?