I have a proposal for timing that I want to share with the community instead of forcing it into place (that's bad moderating). I will post this on the Where The Fairy Flies/For The Sequel forum as well as that is the most popular game and easier to see the thread because of how this site works.

There is a file timer in the games, and as this would be a universal timer and is common to use in other communities (e.g. Sonic, 007 Agent Under Fire, Axiom Verge), this would be a good use, but also a possibly bad use.

Advantages:

• Universal timer - Game-time is more reliable than real-time in terms of loading times and lag (although the 3DS doesn't have problems with these, if I recall correctly)
• Runners without a capture card can post proof as a picture of their file with the time, opening the game up to more people

Disadvantages:

• Runners without video proof may also be able to get away with segmented runs, which would be against the new ruleset if game-time was implemented
• Current runs may be invalid unless they either a) know the game-time or b) use real-time as game-time

However, currently some runners with only split proof have been accepted; this may hopefully address the disadvantages, as using both real-time with splits along with game-time should be enough proof, and may also be able to roughly distinguish the difference between real-time and game-time so that current runs can have an estimated game-time.

These are just my thoughts. Like I said, I think it'd open up the games to more people who want to run it but don't have a capture card, at the cost of a little bit of vulnerability to cheaters.