Yes, there've been new rules drawn up with the AFM (American Federation of Musicians) designed to accommodate soundtrack releases by increasing the number of units sold of an album before the reuse fees kick in, by lowering fees, or things like that. The thing is, though, IIRC the new rules just apply to new scores recorded from the time of the new agreement; older recordings are still subject to the rules in effect at the time.
Since
Raiders of the Lost Ark was recorded by the LSO under very different regulations than those under which the other two were released, a complete version of
Raiders should be readily doable as far as the licensing goes; note it's the one for which there's been an expanded release already. I think the main reason it's still not complete is simply that it's hard to fit much more music on a single CD than the current one has, and they wanted to make it a single-CD set (double-CD sets for orchestral film scores generally don't sell well, apparently, though I'd hope an Indy movie would be an exception). Note also the four volumes of
The Young Indiana Jones Chronicles all feature a ton of music - they're all over 70 minutes long; one of them is over 78 - and they had no problems licensing all that music for albums they knew wouldn't sell as well as the movie soundtracks. It's because the episodes from the show were mostly recorded by overseas, non-AFM orchestras. I believe the pilot,
Young Indiana Jones and the Curse of the Jackal, was recorded domestically in LA, and it doesn't show up on any of the four soundtrack volumes, apparently because of the reuse fees.
But still, anything's possible. There've been some amazing score releases just in the past year that many score geeks were sure would never happen. With all the Indy stuff happening now, this year would be a great opportunity to finally do the first three movie scores right, and I'm hoping it happens.