Show us all the Gameshark code to enter so that there are six top-3 tables (one for each character) instead of one, and it will be considered. Show me the Gameshark code that makes times recorded in Genesis games at all. But, nevertheless, I think the current system ought to stay.
I don't dread suggestions...
Ground rules that make sense. If there is no built-in chart, record as expansively as the game options dictate; if there is one, use whatever that chart records, and don't try to cause confusion by adding extra tracking charts.
So far it seems there are two cases where the above policy is violated:
1) S3TA tracking 1-Lap times. Obviously these aren't saved...but hey, neither are times in the main game; and at least the game is kind enough to list all your 1-laps at the end of the race so you don't have to go to extreme lengths to track them. Plus, it provides a bit of an artificial "weight boost" for these levels to have on the S3 rankings (and remember, it does follow the rule partially, given that you don't have 1-Lap/5-Lap divided by character).
2) Knuckles Chaotix. Consistency with the originals would mandate that each character combo be kept separate, but this is downright impractical. 25 of the levels would then require 30 sets of rankings each, another four would need 20 sets, and all those would increase to 42 sets of rankings if you were allowed to choose Heavy or Bomb as the first player from Debug (and to 56 if you use the extra, unfinished character). Clearly this would wreck the whole format of the webpage (not to mention turn the overall rankings into little more than a test of endurance). Probably much better to say "okay, screw it, Chaotix is a wacky game so there's no need to worry about 'consistency' with the rest" and just pull out some sense.
But other than that, there aren't really any more cases where practical matters outweighed the usefulness of this rule of thumb. SA2 Kart doesn't demonstrate that need either--in fact just the opposite, because breaking the rule in this case would extend the number of charts from 3 to 18, which would look ugly no matter how you did it (because of space constraints for records stored on the site, those 18 would have to be listed in an 18x1 structure, not a 6x3). It would be more likely that those records be split by system (DC/GC) before they get split by character, and that's not about to happen either. At least not that I know about.