During my time as a CM, I've come to learn how diverse our playerbase is in terms of what it's looking for. We have a PvP audience, a PvE audience, a PvEvP audience, and more. All of those players have individual needs, but our primary mode continues to be Random Battles by virtue of it being the most played mode in our game. We have to balance to what people play as a standard.
In games like Diablo or other games when players build personalized power fantasies and play them out, a big part of the design concept is to enable that power fantasy. Thankfully, bots don't care how often they're slain so players can single-handedly wipe away legions of enemies in pursuit of the power fantasy and that is perfectly ok. That breaks down in games where the primary interaction is PvP-based.
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Again, your point echoes what the Naval Training Center idea existed for. A way to pick a favorite ship and customize it a bit. That creates play incentive as long as the customization is small enough to be cool but not game defining. However, players expressed very strong concerns with altering base ship stats (which can also be altered by Commander Skills) and the Naval Training Center was not implemented. Instead, there's a re-grind mechanic which gives players a way to re-experience a preferred grind while working toward a reward for doing so.