You can still take easier missions, they just typically aren't worth doing. You can reset what missions are available by leaving and re-entering the station or going to another one. You want to retire/swap characters when their liberation effectiveness runs low - typically I hit around 40-50%, then do my main mission and retire them. If you need to kill shielded dudes, use a subverter on them to invert/remove shields. Otherwise avoid them or lure them into glitch teleporters, explodable rooms, near glass, etc.