I bring this up because it seems to be a point of uncertainty (or at least curiosity) on the dev team with regards to bomber pilots suffering very high casualty rates for relatively little gain.
If one wishes to preserve the current dynamic regarding torpedoes/bombs, there are two ideas that intrigue me, one of which was furthered by the dev team (and related elements) itself--but I'm very curious about it from an in-story point of view.
So with regards to the 'cruise' missile possibility:
A) It would be like a faster, long-range version of current torpedoes (like, say, the Cyclops); the main drawback is that it would take up significantly more cargo space. It would still have the bomb flag, meaning it can be shot down like any other torpedo, and though it will be relatively fast (for example, 350 m/s perhaps), it would still take a significant length of time to reach its target from a range of five-six kilometers, making its effectiveness when fighter screens or point defenses are capable of interception questionable. The idea is that these would feel kind of like Ares Treb strikes--jump in five kilometers out, launch a salvo of Trebs, quickly jump out--but would not really be attempted or likely to succeed unless a ship's point defenses and/or fighter cover was significantly compromised. Since that is kind of already the case with traditional bomber/torpedo strikes, this method at least results in minimal casualties among the bomber squadrons rather than looking like a suicide brigade.
B) Bomber attacks could still be launched with the target's defenses still up if they were adequately distracted or engaged with other forces--like some space superiority fighters backed up by a heavy assault wing, or a hostile corvette pair. Launching from multiple directions at once can increase hit probability too, while giving the player greater challenge without being overly hard or complicated (you can see what you do wrong, and easily think about how to do better).
C) Might give heavy bombers relevance again if the refire rates for the cruise missiles were kept reasonably low. A heavier-duty version might be doable for the large secondary banks of heavy bombers, something that retains the same capabilities as the smaller cruise missiles but packs a much greater punch (and is thus usually reserved for when hit probability is high).
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As for the drone bombers:
A) What exactly are the complications for implementing such a strategy? Would bombers become cheaper, or more expensive? Could they be made smaller while retaining the same bomb capacities?
B) How much effectiveness would they lose?
C) How susceptible are they to ECM and electronic warfare?
D) Could they morph into hatcheries? Could they perform a gas steal?