1) When using gear (unlike Alex), you have to repeatedly stop and insert it, referred to as "protection." This slows progress and your partner has to then stop and remove that protection as you ascend. After each pitch (think a rope length), you then have to set up an anchor and organize/sort the gear before progressing. So, using and managing gear takes considerable time.
2) Two climbers are usually taking turns, with one belaying while the other climbs.
3) Alex has a level of competence on rock unmatched by us other climbers; his mastery allows him to swiftly glide through sections where most climbers would need more time to think about the moves, analyze the options, etc.
4) Alex was very familiar with the route, with many sequences memorized. Doing the route with less familiarity is like a puzzle, resulting in slower progress as you figure out how to get through various sections.
5) Alex has better stamina with less need for rest.
6) This is a hard route, and many climbers might fall or rest on their gear repeatedly while working through difficult sections.
I'm sure I'm leaving out a few reasons but in a nutshell, keeping it simple (no gear, no partner, no unknown moves, etc.) increases efficiency.
Additionally, once you are going to spend more than a day on a wall you have to also bring along camping gear and additional food, especially water. This means erecting elaborate haul systems after every pitch and slows things down dramatically.
While free climbing, you also need to wait for your partner to climb the same section. Which effectively almost doubles the time.
You don't have that limitation while going solo.
The difference in skill between Alex Honnold and the majority of other climbers can't be overstated. But I think the main difference in speed has to do with familiarity. Alex didn't just go up to this wall and start climbing it. He's done it over and over and over and over again. He know what moves he needs to make and how to do them. You climb much quicker when you don't have to do any route finding.
Honnold climbed it incredibly quickly. Most people take three or four days, this is a very long and very difficult route. If you've ever been to an indoor top rope gym, imagine picking the hardest route and doing it about 80 times.
Honnold and Tommy Caldwell climbed it as a traditional roped team in around six hours while rehearsing for the solo. It comes down to the competence of the team and how well they know the route. I can promise you that Honnold knew every single foot placement off by heart by the time he hiked up to solo it.
3,300 feet of climbing is a lot of climbing. Most non-pro climbers will be winded and in need of a rest after a couple hundred feet of climbing. Also, it is easier to move without ropes since you never have to sort gear or re-coil your rope.
