This certainly can be a problem!
Back in my old 4th ed saga, the "casting from text" rule ruined a lot, not just travel. Since the crafty players had a librarian-type-magus copy a lot of useful spells, they could bring them along on adventure. Since they were just copies, no one cared whether one or two copies got ruined once in a while. And no one spent the time to learn those spells, since it was easy to cast it from text.
Yes, if their arts relevant to this spell sucked, they'd just take time to add Concentration (which was an ability used when calculating exp from reading, so everyone had a fair level in it) or just "pay the difference" in extra fatigue levels. The fatigue was rarely relevant, since one or two levels could quickly be regained with a little rest. The only times I could spoil this, when I made up harsh climates or weather to ruin the parchment, og make time a factor. But it was an uphill struggle, and vary artifivcal to always make up these situations. I didn't do this myself, my maga was a Hoplite, and needed to cast her own spells dammit, not read aloud from a scroll!
The abusive spells were Wings of Soaring Wind, Image of the Haunting Ghost (or something, the spell where the caster projects his talking image to an arcane connection. Essentially a telephone to another magus, once the relevant arcane connnections were set up. Also teleportation.
However! I set up several long, far expedition-type adventures. No one used flight or teleportation there. Perhasp they took the short cuts from central France to the Med, but sailed to through the Greek Isles all the way to Egypt, and even went through Constantinople one time. They visited some mythic places of their own accord, and I made up a lot of intertwined story threads on the journey. Plus, their original mission was one of following vague clues, each one opening up other leads on so on. Most of the adventures on the jouney were of the same type. It went quite wel.
But, here in my new 5th ed saga, all those "casting from text" problems are gone. I'm debating to myself whether to actually use the optional rule from Covenants about Casting Tablets. If I do, I'll make the whole process very adrous and rarely usefull. Perhaps the tablets need to be of inconvenient size, shape and material. Perhaps they need some vis or precious materials to "imbue". I'll make sure they're very rigid in their use, and that it takes tiiiiiiiime to cast.
Either way, the travel problems still exist. Since the new saga is actually a spin-off of the old (my Hoplite maga is the only conversion), the magi are 30 years out of gauntlet. They can easily have flight or teleport spells. Luckily not many do, but they'll get there. If one can travel easily, the rest also want to.
The most annoying thing is, one player plays a Flambeau Giant Blooded Corpus specialist. He is made for melee combat, with a heavy chain mail and a great sword. He has a whole deal of boosting and protective spells. Everytime he senses trouble, he activates everything. And at the first sign of fighting, which he reckons he can't win in one round, without taking damage himself or even risking anything, he instantly teleports (he has a Range: Sight version!). He has Flawless Magic, so I can't even hope he botches, it is very unlikely. ALso, this particular player has a history of simplu not rolling 0 on the botch dice. He once rolled at least 14 dice, for casting a ritual from text (in 4th ed), and still no '0'! Spoilsport!
Untill now, he has simply not gained anything from these fights, he teleports out of. If someone ambushes or surprises him, he'll perhaps take a little damage during the first attack (but he is boosted beyond human standards), but then he'll feel he's risking something, and surely vanish.
To limit his sight, would remedy this. But he always uses vision enhancing spells, but smoke or mist is good. Enclosed spaces also do the trick. Since he is Giant Blooded, I ruled that he's so large, than one or two small critters clinging to him come along in the teleport, since their mass is insignificant compared to his own and his war gear. Because his Corpus spells are boosted in magnitude, to allow Individual to affect a giant!
Back on topic:
If the easy travel for the PC magi seem to short circuit stories, have them not just be about something at the destination, but something during the journey. If they need to visit several places and check up on leads, they'll have to stop. Have a lot of stope be in difficult places; inside a major city, a regio, another covenant etc.
Or, use the easy travel to an advantage! Have stories reach far away, and for a long time. Impose limits on the distance teleportation works. Hit the fliers hard with fatigue for long journeys. Make difficulties for them, they'd have to avoid major settlements, or large bodies of water, for safety. Have the wather fould things up. If you need to go to Africa, you'll propably stay for more then the afternoon, then you'll need servant, camping gear, provisions. Limit the usefulness of a simple arcane connection. If magus A flies to Ethiopia and picks up rock, who is to say it's a perfect arcane connection? A connection to what? For how long?