I think the issue here is not the idea of pilotless ships, just the inconsistent implementation. Ships should either require pilots or they shouldn't (with the exception of canonically pilotless ships always being pilotless).
As a side tangent, I feel that inconsistency is one of the major flaws of this game, especially compared to other games. If you think about it, it explains a lot of the frustration from the community. For example, GP. It used to not matter how good all of your characters were. Then, it was good to have a really high GP, and it was good to level up bad characters. And finally now it is bad to have a high GP and any leveled up bad characters hurt your ability to be competitive. Another example is currency. Some stores have been abandoned (GW store). Some stores have been completely reworked (SS). Some stores seemed to be for one thing and then turned out to be for something else (GET). Having a goal set before you and then having it change just as you get close is very frustrating. For a game that is all about planning and resource management, it is very hard to do either of those things if the fundamental structure of the game is always changing.