IMHO, anything and everything that must be repeated without offering a challenge of any kind should have the option of automation.
Or, it should have a challenge added.
Make travelling a distance longer than - say - 1000LY increasingly difficult (up to a maximum, not just increasing forever). So you can go Sol-Pleiades-California okay, and you can hop around between deep space bases within a few thousand LY of Sol, without too many issues.
Travel to Colonia? Well, it's a few thousand LY between rest stops - expect it to be a little tricky to make it to the next highway base, especially once they start really thinning out as you get past Rohini.
Travel to Beagle Point? Actually requires a serious effort - maybe even teamwork for all but the most skilled explorers - to travel that far without resupply. And then you still have to get back.
Make it not just a matter of honk-jump, so you have to stop at least every few systems to deal with something (be that fixing wear-and-tear, scooping from a gas giant, picking up materials to repair modules, etc.) and the question of "why can't we automate 100 consecutive honk jumps" goes away, because no-one is ever doing that anyway.
Make fuel scooping from stars like it was in FE2/FFE - a really dangerous "last resort" option which guarantees damage to your ship even if you do everything right. Sensible people scoop from gas giants, which is still a little tricky but safe enough once you get the hang of it. People travelling shorter distances just pack extra fuel tanks instead of a scoop, and do some semi-economic routing.
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The problem in this case with automating it is the nature of the automation. It shouldn't be faster to automate the travel than it is to do it manually. But large chunks of the current travel time are loading screens, so firstly should get faster as hardware progresses - and on average have, since 1.0 - and secondly it makes no sense to show ten loading screens to load one system.
If you can travel while logged out at a "as if you were honk-jumping" rate based on your fuel scoop and FSD, you can just set it, go to bed, and get up 20,000 LY away ... which is a solution, but then why can't you autotrade overnight and wake up 8 hours * trade route * tonnage richer? It's not as if basic A-B trading is difficult or interesting either.
Conversely, if it's just a basic "scooping computer" which flies around the star at a safe distance until full then automatically continues the route, how is "waiting for 5 hours not pressing J" better than "waiting for 5 hours occasionally pressing J". It's basically still the "log out and wake up richer" question except with the extremely marginal risk that something will interrupt the autopilot and you wander in to a rebuy screen in the morning.
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So *even though* it might be a bit late to add some challenge to long-distance travel, I think that's the direction Frontier need to go in. They've already multiplied jump ranges by ~8 since the 1.0 release and people still aren't satisfied with that - and won't be until you can jump 10,000 LY at once. So they need to try something different.