Yeah, this is something that should be added to the rules, but I guess we haven't yet because it hasn't been asked too often.

Unfortunately, we don't allow USB loaders or emulator at this time. There are two major issues shared by both:

1. If the software doesn't try to emulate accurate load times, the speed will depend on your particular USB/SD device (in a USB loader's case) or on your computer's hardware and configuration (in an emulator's case). So even if it runs slower than console for you, it could be faster for someone else running the same software.

2. If the software DOES try to emulate accurate load times, it's still tricky to define how much load time accuracy is "good enough" for the leaderboards. At the very least, more testing would be needed before allowing anything. So far the only thing we've tested in detail are disc loaders (Gecko is fine, Neogamma isn't): http://www.speedrun.com/smgalaxy/thread/7hyr7

I've seen discussions in other communities about allowing this stuff when a player's time is above a certain threshold (for example, 3h15m Any%). I think that's a decent idea, but it would need some discussion before updating any rules.

On the idea of taking a time penalty for running a USB loader: I can't remember much discussion about this, but I personally don't think this is viable because there are at least 1 or 2 variable load times before every single star, making it quite a pain to calculate an accurate penalty. And I wouldn't be a fan of adding an arbitrary penalty like 2 minutes, since it'd be, well, too arbitrary. It's best if the leaderboard reflects actual run times.