I'm really torn. On the one hand, it's a lot simpler to balance if every ship's weapon mounts and systems are pre-defined, and as a result every ship is distinct, making the choice of ship much more meaningful than otherwise. On the other, I'm always all for upgrades and customisation, and letting the player conform as much of the game's content as possible to their preferred playstyle. I do think there should be some pretty severe trade-offs, and investments and costs required, to make it another thing to flesh out the mid-late game, and also some hard restrictions to prevent the creation of absolutely overpowered ships. Phase tech especially would ideally be restricted to ships built around those systems, but you wouldn't be precluded from replacing them on those ships. Thinks like a chance of applying D-mods if you haven't invested in the pertinent skills or equipment. "Your crew stripped out the phase skimmer, but took some important components with it. Your ship's Peak Performance is now 50% shorter" (Unreliable subsystems) for example.
But yeah, if it were up to me, I'd replace the small mounts on my Wolves with ballistics for some longer-range kinetic damage. But then we come back round to the argument that it then may be too powerful - The Wolf's already a very powerful ship for its size, cost and upkeep requirements; the restriction of all its weapons to energy serves to limit its versatility in the types of targets it's effective against. Some mods already break this by adding small HE energy weapons, and kinetic missiles that are miles better than Sabots, meaning in addition to its supreme mobility, I now have a lot more firepower that in vanilla, is otherwise traded off.
All this aside, I would like to be able to choose the ship's skin where applicable, I don't like having a non-uniform fleet if I can avoid it.
There's a problem though - I think the biggest hurdle with this suggestion is the technical aspect. As far as I'm aware, any variant of a ship is considered a different ship as far as the game's concerned, (D)s produced through combat notwithstanding. This is why those ships with destroyed/downsized weapon mounts or reduced OP can't be restored to the stock version of that hull, and why destroyed weapon mounts can't be applied dynamically in the same way as other D-mods. I'm not going to pretend to know what it'd take to implement what'd essentially be modding ships on the fly, but I don't imagine it'd be easy. The question then comes down to whether it'd be worth it for a huge but questionable shake-up to the possibilities within the game.
The creation of more variants, and allowing players to refit ships to those specs would be the best way to go about it imo, as done right it could maintain the balance that currently exists. Say, Wolf (B) - has had its medium mount replaced with a hybrid, and one of the small mounts is replaced with a small ballistic at the expense of the other two.