Two things I think would improve alliance missions and increase participation.
The major problem now is that people aren't showing up for missions. To combat this and make it more interesting, alliance teams should be able to wager loot that is won/lost by each participating base. Could have various lvls of wagers, but they all would have to be significant enough to make sure people show up.
Second problem is time commitment is too long. I think max search time is 15 min. before time out. 15 min for set up. 1 hr battle time.