Well ya, but that's not a problem, since someone could just spend a few minutes to create a saved game.
Having the saved game on the cartridge seems like the best solution. Nothing's offical, though, but if that sounds ok with you, I think that's how it should work.
All it's doing is cutting time off the game clock, but not in real time. That would be ok if everyone could do it, but they can't. My point is that it's the same run either way, regardless of what the game clock says, so there's not much point cutting off time to the gameclock if everyone can't do it.
Now I don't know what to do. The only way to delete the file is to have Pokemon Stadium, so it's not like everyone can do it. It's kind of an unfair advantage for an extra 40 seconds cut off.
The rule could be that you have to start the speedrun with a saved game, but that kind of seems weird.
It could also be that the speedrun is timed manually so you could put in your name and not be penalized. The ingame clock works great, though, so that seems like a shame and a hassle.
The rule that you have to start the speedrun with a saved game seems like the most practical solution, but it not great either way. I hope that makes sense.
If the clock doesn't start until you gain control of your character, wouldn't you save more than 50 seconds? Isn't the opening text longer than 50 seconds?
Really? On my Pokemon Red cart, I just left the game on for about 10 minutes on the opening text. When I came back to the game and got control of my character for the first time, the clock read 11 minutes. Is there a difference in the versions?
Well, I just improved my Pokemon Red run to 2:19, and I can make at least three minutes of improvements before reading this. Anyways, 1:59 could be done if Japanese text is really that much faster, without any big change to route.
I also have one improvement that you didn't use in your run. When your about to fight Erika, you have to vs one trainer first. You followed the route I did in my old run, and vs'd the trainer with 3 pokemon. Well, if you follow the wall to the left, and enter from the left side, you can vs a trainer with only one pokemon (the egg one). Anyways, it falls to a single ice beam, so it's definitely faster. The only disadvantage is that you lose some experience. So, this should save you 30 or so seconds, unless I'm overlooking something.
This would save a good amount of time. I usually have to fight two random battles in Mt. Moon, so I can get bite before I vs the trainer with two oddish's (before Bill). With Mega Punch, I could skip those battles and I could finish a few battles a little bit faster.
I also didn't use Abra to teleport around, which could save a good amount of time. Hmm, sub 2:15 may be possible for a normal speedrun.
Anyways, I hope my wee bit advice helps you. Good luck with your new run, well, a TAS doesn't really need luck. :)