I guess to answer the Netflix time/refleet time issues, while keeping up an incentive for the player to not just throw ships willy nilly at something that might work, I'd consider something like the following:
- Metal stockpiles are replaced entirely by 'metal rate', which acts like an Energy but for ships or structures that produce other structures. So if you have a metal rate of 1000, you can support two engineers running full-time, or a shipyard, or ... So essentially, the time factor to refleeting is a single thing - the rate at which shipyards/etc produce - rather than being a combination of two factors.
- Superweapons, Zenith Trader stuff, etc is paid for by a separate non-self-generating pool of resources that come exclusively from salvage considerations. The idea would be, salvage isn't about scavenging metal or commoditizable resources, its about scavenging bits of non-reproducible technology, encryption codes, analyses of enemy ship performance, etc. Those things are needed to repair things that the humans can't themselves make from scratch (golems, etc). So this encourages the player to be successful at smashing enemy ships at strategic locations that are set up to efficiently gather salvage. This could be tied to low-cap structures ('salvage nets'), so manipulating the AI to send a huge wave to a collection point would be a basic strategy.
- On the AI side of things, the design consideration was to have a short-term recoverable risk to the player in response to a bad move, to avoid permanent stalemates. But this could be done in the sense that the AI understands that its cheaper to finish off a weakened enemy than to sustain a perfectly constant degree of engagement with enemy forces. So what if the advantage during an assault (something like, the change in the relative size of the player's forces to the AI's local forces) generates points of 'temporary AIP', which contributes to the reprisal, and then quickly decays (to prevent 'gotta wait for the TAIP to go down')? Basically, the AI decides 'yes, this isn't that big of a threat compared to the other thing I'm facing, but this is a more efficient moment to deal with that threat, so its worth a little extra consideration'.
- If you want to keep the sense in which the player can't be rebuilding his fleet during the reprisal itself (to encourage potentially leaving a portion of forces behind for defense, say), maybe allow the AI to have something sort of loosely equivalent to the player's ability to deploy warheads - the AI can sacrifice points of AIP (either real or temporary AIP) to briefly shut down the player's metal production in a system, thus forcing some of their shipyards/etc offline during the reprisal. The AI will obviously be much more willing to sacrifice AIP if its just temporary AIP, adding a second layer of danger to over-reaching.