Well, they DID skip large amounts of the trip.
Everything between Pluto and Saturn, and Saturn and Mars was ignored.
Though it was stated that they'd been under pretty regular attack between Saturn and Mars, which may have prvented a stopover at Jupiter. And they were likely too busy setting up a counter-offensive at Saturn to refuel.
Unless they were scooping particles out of the rings, but I'd think the scoop would've been on the bow of the ship, which was pointing upwards during the Saturn operation, if I'm not mistaken. And as the Macross wasn't originally designed to be a long-range vessel, I have doubts as to whether a bussard scoop was there to begin with.
But Uranus and Neptune were untouched. If they were capable of refueling from gas giants, that's where they'd've done it.