Ascended Fanon: Andrew has admitted to getting as many plot ideas from the Wild Mass Guessing on the forums as the user commands themselves. Homestuck now almost entirely runs on this, since the suggestion boxes have been closed.
Approval of God: Pretty much any and all fanworks are approved of by Andrew Hussie, especially fan adventures which even have their own site in the form of MS-Paint Fan Adventures.
Doing It for the Art: More of the writing than the art itself. The is art fairly well below Andrew's skill level but he clearly enjoys writing the story solely for the story.
Around the time that Problem Sleuth ended, an impressive number of member-run MSPAs started showing up in the MSPA forum. For his part, Andrew is highly supportive of these: participating in some, linking to the more popular ones in a newspost, and creating a separate subforum in his forums to organize them.
MSPA's influence has become so broad that a number of comics with similar formats such as Silent Hill: Promise and Aetheria Epics have sprung up independently of the forums.
Funnily enough, the grandaddy of these fan MSPAs, Bird Wizard, had a suggestion from Andrew Hussie ("Squawk like an idiot and shit on your desk.") that made it into Homestuck (though the character resisted it).
Schedule Slip: Rarely an issue. Regular webcomics might have 3 or 5 pages a week, with some having as many as 7. MSPA averages about 40. In a single day there have been upwards of 30 pages. Andrew describes MSPA as less of a job and more of a lifestyle; he literally does little other than update constantly.
However, pages of MSPA might not be comparable to pages of most webcomics.
By his own standards the later half of Act 5 Act 2 of Homestuck suffered heavily from very sporadic updates and pacing problems. Switching narration over to Doc Scratch was designed to relieve this, and that started to drag on as well! Seems to have recovered fully with Act 6 however. And it should be said that even during this "slip", he still updated more frequently than normal web comics.
Writing by the Seat of Your Pants: Interesting use. In Homestuck, Andrew planned out the entire process of Sburb, and the end result before even making a single page, but the way the story shows that process is completely improvised. Concepts such as the trolls, the exiles, and the entire Apocalypse were made up more or less on the fly. Applies to the art, as well. Andrew has admitted to creating some character designs shortly before they were introduced, such as the guardians. Andrew admitted the basic story plan for Homestuck was from the outset: Make crazy shit up. It's worked surprisingly well so far.