It's handled badly, though. As it is now it's just an inconvenience that stops you from doing what you are doing for a couple of minutes while you sit in the corona, fiddling your thumbs, watching the gauge go up and perhaps keep the heat in check once in a while.
It would be so much better if the number of jumps on one tank of fuel would be much, much higher (say 1,000-5,000 light years), but the refueling process would be much more involving than it is now. The refueling process could be a mission in itself. It could require you to disable all unnecessary systems, to plot a safe course through the corona and its mass ejections and flares that you'd need to maintain etc. There are quite a few cool things that you could do with the fuel scooping maneuver. Things that would make it a more rare but much more exciting occurence, especially out there in the middle of nowhere. It should be a risky procedure that gives you sweaty palms... but unfortunately that's not the case.
Opposite opinion from my pov.
It's handled fairly well - improvable, sure, but not badly at all. It takes minutes because that is the choice you configured for your ship. Using a 5A scoop for example on a an Asp or ship wth 32T fuel tank, it takes seconds - most the time just doing a 'dip and dash' is enough - won't refill tanks fully, but every time hyper out to a kgbfoam star, I just dip and scoop while FSD cools down, then jump again soon as reset.
That allows for quite a long way of extending chain jumping until finally have to come to normal full refuel scoop - which again with a 5A scoop on 32T tank takes nowhere close being counted in minutes, but still in seconds- although for a full near empty to 32T refill, it takes something like 30 sec ballpark'ish - don't quote me on that, will have to re-time it next time but it is for sure far less than a minute even for full refill.
Second - common sense in a scifi game is sort of moot, but on other hand, past tech progression has shown that complimentary techs always paces each other. So if we propulsion tech is what we see as is in ED universe, then the complimentary refueling tech for that propulsion tech has to be equally advanced or close to it. Having propulsion that allows crossing entire galaxies and yet have the complimentary tech of refueling be much more involving where it is a "risky procedure that gives you sweaty palms" seems far out of whack of plausible tech progression.
And again not that common sense in scifi has to matter - but we either have highly efficient jump drives or we don't. e.g. the tech is so miracle magic tech that somehow we compress and scoop from the interstitial space between stars some form of 'regenerating' fuel or are able to trigger such large energy reactions that a small amount of fuel allows vastly long distance travel - either say, we have this tech or we don't
But if we do have that vast distance without refueling tech that allows jump drives to be that efficient, then the refueling tech would have to be as likely advanced as well. It's hard to plausibly ascribe something as achieved via science to allow that level of jump tech, but still be so primitive in refueling that the very act of refueling is a sweaty experience.
What I would like to see is different refueling options given. The scoop of hydrogen based stellar objects like stars is fine, but I'd also like to see slower, but differing options like theorized ram jets that scoop free floating hydrogen from the system matter as well as less dense interstitial space between star systems. The only gap I'm aware of that free floating hydrogen would be difficult to theoretically gather would be in the interstitial space between galaxies, but that's moot since ED is purely our galaxy only.
For that matter, it's odd to think by 3301 that complete fusion recombination tech isn't in place. Option 3 - need fuel? turn some of your cargo matter into fuel via fusion, ala Back to the Future mobile.
My only wishlist for ED is that the amount of plausible tech missing given the other extremely advanced tech we see leaves lots of rooms for additions as well as head scratching confusion why the heck can't we do X, if we can clearly do Y?