"[Think about how the crash sites disappear after a few days -- why do they disappear? It's certainly not because of rednecks with shotguns feeding sectoids to alligators"
"Hey Billybob them Sectoids are in da fields again, get my gun"
Sounds like im not the only person who ponders these things. As stated above , my thought on the missing ships was from a organised Cell of human that works with the aliens. If these are normal human helping the aliens for there own financial goals or Clones created by the aliens is up to you to decide . To me if we shoot down a UFO it would be crazy to send another one that will be picked up on radar to retrieve them ( as then i need to shoot that one down also) so this would be where the terrorist cells come into play. Have them Spawn onto the edge of a battle map at a random turn to HELP there alien friends .
As for your other thoughts they sound like some winners to me.
Maybe its time we started getting a group of interested people together on this page to start planning out a official Openxcom MOD version of the game. Start planning out what new weapons we want , battle types , new enemys etc, agree on what direction we want to go and as a team start working towards it. Personally im terrible at graphics but i still have a go as i have a dream of xcom that has not yet been fully reached, that's why i started experimenting with the sprites. I don't want to change the feel of the game i just want to add more content