Pathfinder is based on the logic of "the adventuring day." You have X encounters, deplete Y% of resources, then sleep and do it over again. That works great in the dungeon, but it's harder to string resource-draining encounters together in an overland adventure. Justifying 3-5 run-ins with wild animals and bandits stretches credulity, not to mention the fact that flight and teleportation can flummox any attempt at planning.
All that said, how do you like to structure your adventures when it's all about travel? What distinguishes a "good travel adventure" from a bad one?
Generally I don't think that travel should be so insanely dangerous that it saps the resources of even a low level party. In most cases that doesn't make sense at all.
Going into a very dangerous environment is different of course. You might well have 3-5 run ins with wild animals, tribal headhunters when exploring Skull Island.
Flight and teleportation can change things, but they don't have to change things all that much. For the most part, teleportation isn't going to work in an exploration setting and if it is just a 'go from A to B' situation, then teleport is faster in game time, but not real time as routine travel generally shouldn't be particularly worthy of playing out anyway.
Unless there is a reason for the journey itself to be particularly important as an adventure (and that reason should give you why there are significant encounters) then let it slip into the background where it belongs.
Back in the halcyon days of the 70s, going on a "wilderness adventure" was much like going on a dungeon adventure, simply with a different sort of map. Players would explore and discover the blank page, finding monster lairs, towns, evil overlord castles and so on, always peppered with random encounters, often specially arranged by the DM to disrupt resting periods and thus defeat at times the "15-minute adventuring day" phenomenon.
While I've got a lot of nostalgia for that sort of adventure, many aspects of it don't make a lot of sense. For starters, why would the map be blank? Surely folks have lived here for many generations, and although not everybody would have a detailed hex-by-hex map of the terrain, features, towns, rivers and lairs, many of them would have a fairly accurate general idea, and some of them (notably folks going into adventuring careers) would have very specific knowledge of at least a part of that wilderness.
These days, to have a fun, dynamic and effective wilderness adventure, the DM should start by asking himself a few questions, especially what the purpose of the PCs' travel experience is intended to be:
1) Is the goal simply to go to a specific location?
2) Do the PCs need to find something specific (a person, a treasure, a monster, a place of mystery)?
3) Do the PCs have a special mission, like making the town safe from marauding goblins, or scouting the advance of an invading army?
4) Is there some hidden information, ally, mystical grove or clue to a mystery that the DM wants them to "stumble across" during their trip?
The list could well continue, and depending on the answers to these sorts of questions, the DM's preparation of a wilderness adventure gaming session will be quite different.
Lastly, as noted above, so much will depend on how high level the PCs are, and what access they have to knowledge and survival skills, different modes of transport (horseback, riverboat, flying carpet, teleportation) and most especially what sort of plan they've hatched for reaching their goals.
The link to The Handbook of Heroes didn't work for me, due to a gratuitous "<br />" line break statement in it. Try Handbook of Heroes: Travel Time.
A related comic is Order of the Stick #145: Wizard Explains Random Encounters.
When I run travel, I turn the random encounter table into a series of planned encounters that give a tour of the area's monsters. If the table says giants live in the area, then I plan an encounter with a giant. My players learned that if they send scouts ahead, then the scouts might spot the giant from a distance and re-route the caravan to avoid the giant. That way good roleplaying by the party can earn the XP of the encounter without the risk. The minimal encounter provides all the plot necessary for the travel adventure, for example, it gives a sense of time passing and of alertness against danger. An actual battle with the giant would serve no additional purpose. Though the giants are hostile, they are not real enemies of the party and fighting them would not strengthen the plot.
The Handbook of Heroes link mentioned the Jade Regent's caravan system. Jade Regent is about escorting the last Amatatsu heir from Varisa to Minkai, so caravan travel is important. When I ran Jade Regent, I asked my players if they wanted to use the caravan combat rules, and they didn't. Thus, I ran their random encounters in my usual pre-planned fashion.
I had doubled the number of heirs for my Jade Regent campaign, because the main heir, Ameiko Kaijitsu of Sandpoint, was too powerful for low levels. Instead, her half sister, Amaya of Westcrown, was interested in the journey and Ameiko stayed behind in Varisia. However, after the party made a three-month arduous journey over the north polar ice cap in The Hungry Storm, I decided to restore Ameiko to the group.
Forest of Spirits Module
As they arrived in Hongal, they had a surprise addition to the party. Amaya had been secretly giggling about her surprise for two weeks, enough that other party members were making Sense Motive rolls. Upon reaching ninth level, Fighter 1/Oracle 8, Amaya had learned Sending. In addition to giving free messages to the passengers, she talked to her sister Ameiko every night. And invited her to join the party.
Four months ago gametime, Ameiko had left the Jade Regent party to help her Rise of the Runelords friends. The Runelords heroes were so bad at leadership that when they conquered the lost city of Xin-Shalast, they asked Ameiko to help them run it, since she had successfully run an inn. Seriously, that happened during that game. Alas, Ameiko became an assassination target for the evil characters vying for influence in the new government. When the Rise of the Rulelords group planned to visit Irrisen for The Witchwar Legacy, Ameiko decided that she needed a nice safe vacation fighting less dangerous creatures, such as oni.
Ameiko (leveled up to Rogue-rake 3/Bard-thundercaller 6) carried the Amatatsu Seal and its Warding Box. Her 17th-level wizard friend made her a storage amulet that shrunk it down in a hidden compartment. The lamia wizards of Xin-Shalast made +2 Amulets of Natural Armor for everyone else, physically identical to Ameiko's storage amulet. Because the Amatatsu Seal could not be teleported, another friend flew her over the Crown of the World in one hour at suborbital velocity, a journey that had taken the Jade Regent party three months.
Sometimes slow travel is appropriate and sometimes fast travel is appropriate. The party needed the dangerous journey over the northern ice cap in order to level up. Ameiko didn't need that adventure to level up; instead, she had some off-the-scene adventures in Xin-Shalast.
Focusing on combat encounters is a mistake, in my opinion. If you're trying to create an adventure focused around an overland journey, then you want to focus your efforts on making the journey itself challenging. If the only way you can think of to do that is to throw a small army of enemies at the party, and they're hitting each of these encounters perfectly fresh, then the journey you're presenting isn't really challenging for characters of their level in the first place. If you did that job right, then adding a combat encounter to the middle will spice it up and complicate an already challenging situation.
Every additional level makes player characters more powerful, but it also gives them more options as well. Those options will allow them to expedite their travel or bypass obstacles along the way. If they don't need to use such abilities and can travel passively then that's what they'll do, and they'll remain perfectly fresh as a result. You must present them with challenges that demand the use of such abilities. This can involve scouting dangerous routes through uncharted wilderness for a shortcut, riding through the night to utter exhaustion, or even just burning through all your spell slots eking out a little more speed. Put the destination in a difficult-to-reach location ("one does not merely walk to the Peak of Despair... literally, it's sheer cliff for much of the ascent!"). Give a time limit (and make it a meaningful one! Any 1st level commoner can buy a horse and ride for 8 hours a day along the beaten path). Give the players the general vicinity of their destination but make them explore to find it. Saddle them with much less capable NPC's that they have to escort.
Doing a good overland travel adventures is hard because you need to be very keenly aware of what your party is capable of to present an challenge that is appropriate to those abilities. There is no CR system to eyeball the difficulty presented by an overland journey, and almost no one builds with it in mind so two characters of the same level can have drastically different abilities to contribute. It takes a degree of system mastery to understand how their spells and abilities will help them overcome these kinds of challenges and balance appropriately against that. However, you don't need to push them to their limit, just hard enough that they take it seriously and flex those muscles.