I think ultimately it's a bummer, but there's no way around that when you have 5,000 products, the kind of sale you want to do is different.
It doesn't make sense to discount 90% if you're not going to do somewhere around 10 times the volume you would at full price, or around 5 times the amount you would do at 50% off. Obviously no one is buying stuff full price during the sale event, but I'm skeptical that people are buying random turd indies 4x as much if they get a deep discount than a standard one. I say somewhere around because it's OK to be a bit of a loss leader to drive volume, awareness, etc. But you certainly don't want to be giving away your business.
I do think if you're the featured, front page sale, there's some likelihood you'll achieve that. But if only say 60-70 games are, out of 5000, it's increasingly not the relevant way people are doing business with Steam. The sad thing is if you're one of those tiny indies that got plucked from obscurity and made buy-a-house money off a day of sales, you won't be able to anymore.
I think what they'll try to move towards is something like a personalized front page. A handful of titles from your wishlist, a handful of big titles, and a handful of up-and-comers, highlighted for you. So your front page isn't my front page. And that's probably a good thing. It will mean fewer crazy breakouts, but the tide should help match people to the games they are most interested in and help ensure that the people making smaller, less popular games aren't discounting for nothing.