Changing to multiple-mission model would require gutting a lot of mechanics... like, currently the loot is immediately teleported to the base. Truly, this system would have to be gutted anyway if we ever wanted UFOs actively intercepting Skyrangers. But while normal loot can be stored onboard, what about Power Sources, Alien Alloys etc? Maybe it's not the Skyranger what does the recovery, though... A special automatic loot recovery craft? Or, simplier, loot is crammed into the Transfers list?
Also, it'd seriously lessen the need for more than a single x-com craft. Plus what to do with heavily wounded soldiers? Right now they fight till the end, but during a flight to a new zone, the adrenaline would've worn out... True, they could be simply incapacitated... maybe extra missions should cause random health damage to all soldiers (because overextension)? This should be enough to balance things out. You can do multiple missions, but your soldiers may end up spending next few days in the hospital, and your wounded risk dying.
And, for people who have certain ruthless mentality, "force soldier deployment" option. You can haul a wounded soldier out of hospital... and he'll immediately suffer, say, random 5-20 damage... "You said you don't care what soldiers want, Commander, the grim reaper said he doesn't care what you want"