The SDCC set sold out, but it wouldn't be fair to compare that to a normal mass-market item. It definitely had a small run, I'm guessing quite a bit smaller than even the current Amazon exclusives. The Lost Wave was also farther along in production (it was Wave 5, correct?) so there was an existing investment in sculpting. Additional sets would probably cost more for Hasbro to make (depending on how far along in the process figures were) while at the same time becoming bigger gambles (too many Indys? too obscure background guys?).
At this point Indy 5 would be the best chance for another figure line. I really hope that does come to fruition. I actually liked Crystal Skull *ducks for cover*, and I'd like to think that Hasbro is better equipped to handle a movie line like Indy now.