After reading the responses here I had a somewhat vague idea, sorry if this doesn't cover everything as I only thought of it today
Assume you're on the OoT any% leaderboards
You see the following:
Fastest Nintendo 64 time is 20:44 by Wallis_Reflect, click here for N64 list
Fastest GameCube time is 24:19 by DeppJay, click here for GCN list
Fastest iQue Player time is 18:51 by Cosmo, click here for iQue list
Fastest Wii VC time is 19:00 by skater82297, click here for VC list
Click here for unverified times
Below this you see the main leaderboard (master list), which is a combined list of the first 4 of those links.
Unverified times wouldn't appear on the main list. Emu runs wouldn't be verified. Runs without videos wouldn't be verified.
This would allow the following:
Combined competition as we have now (allowing all official releases on a master list)
Supporting competition on a console by console basis by listing the times at the top making them more attractive than the many current filter buttons.
Still allowing emu players to submit but they wouldn't appear on the master list.
Increase the legitimacy of the leaderboards by require videos for verification/appearing on the master list.
We could also set some reasonable standards for verification like requiring direct capture and the video in one piece.
I think these steps would go a long way to improving the state of the leaderboards and would put less tension on getting either an iQue or VC-J.
You could take it even a step further for example, by clicking "N64 list" you now have options for NTSC-U, NTSC-J, and PAL.
This is a bit ambitious and I only thought of this today so forgive me if I didn't fully think this through.
Perfect.