- Discarding scrap to pick up other scrap/parts after a battle
- Selling/buying/replenishing/restocking/swapping/installing ship components and cargo
- Using warpgates without operating them from inside (and bringing Chaos to max value instantly)
- Skipping warp-jumps
- Taking or refusing Long-range communication missions/orders
- Moving cargo around
- Assign talents for bots
- Plot course on the Starmap
- Probably something else I managed to forget
1. Mark himself as "AFK" so the game would know he wants to delegate. At minimum, marking himself as AFK should let the other (bots excluded) crewmembers vote to skip - if 100% non-Captain, non-bot crew members want to skip (F8 would suffice), skip the jump.
2. Delegate separate tasks from the list above ("Weapons officer, you are in charge of buying/selling ship components", "Engineer, you can repair us", "Scientist, handle the long range communications", "Pilot, you toss out scrap one by one after we are full and need to pick something else up", etc.). Most of my Captains are newer to the game than I am and/or trust me enough to make rational and optimal choices even though I'm the Weapons Officer (and I still consult everyone and ask before committing to a decision). It would make it vastly easier for the Captain even if he was not AFK.
Captain could then go AFK (that Real Life sometimes...) and the crew could continue on the tasks/path set by the Captain. Or, even the Captain wasn't AFK, they could help him with whatever would be needed.
Please also see Easy and fast shop QoL upgrades for a non-mutually exclusive suggestion for helping the Captain with shopping.