Turn some of the non-mission exploration site finds into unique one-off missions
There are a lot of short blurbs about interesting encounters your troops have in exploration sites that don't result in missions. A lot of these would make excellent one-off missions that would break up the monotony of scavenging/ambush/defense missions.
Just to give an example, there is an exploration site where your team finds a lake that appears grown over with sickly, flaky skin and has some kind of disgusting pus orifice at the center and some reluctant Synedrion scientists studying it. The player could be given the choice to:
a) drop a bomb down the hole (+NJ, -Syn/Anu favor), which would lead to a mission in which you fight over the disgusting lake to drop the bomb, then race out as quickly as possible before the bomb goes off.
b) investigate the lake further (+Syn/Anu, -NJ), which would lead to a mission where you escort a Synedrion scientist as you fight over the disgusting lake to collect a sample from the middle. The scientist would then inform you that the lake is loaded with mutagen and weird algae (food) which you could harvest, but doing so will attract more Pandorans and agitate the weird flesh organism that's grown over the lake. You could then stick around with the scientist to harvest mutagen and food for up to so many turns, or nope out of there immediately after collecting the sample. Bonus points, create a new and unique mutation and present the player with an option to chuck one of their soldiers in to incubate over several turns to get that unique mutation.
I think there's a few things these kinds of missions should try to do as much as possible:
1) Be different (this one is most important)
2) Offer good rewards
3) Don't be mandatory
4) Bring the world to life and explore the game's setting, even if it doesn't advance any larger plot
5) Try to toss in something unique as often as possible (a unique reward, a unique enemy, a unique environment, a unique mechanic, anything)
If anyone can think of other exploration site blurbs that would make great missions, I'd love to hear your ideas. The New Jericho haven under siege from exploding ducks comes to mind as well.