I think WB should go for a 3-way deal - give Cavill a long term deal i.e. 6 pictures+cameos etc, producer cred, reasonable $$ that WB is not short of
Sign McQuarrie as the combo and give him the $$ and pet projects he wants
Get McQuarrie to get Cruise as Hal and ask Cruise to do what he does best - helping studios or independent directors to get their projects off the ground Oblivon/Jack Reacher style, and apply to a GLC that's in development hell since 2011. Have McQuarrie as producer/part of the writer team with Johns or others, and Doug Liman or someone of Cruise's choice as the director. Once you sign Cruise I think he'll have plenty of control.
Since Sup and GLC will be worked on by the same big family/team, they have the freedom to cross pollinate in the future if these directors want/need, and WB get 2 difficult franchises off the ground in one go, with actors/directors who have their clout and can control the ships.
Other option if for Cruise to be Lex Senior to stay with McQuarrie, or Cruise team up with McQuarrie and dump Cavill lol. But I think Cruise is generous enough to get a new franchise off the ground than hurting other actors.
and IF we do get 2 franchises off the ground quickly, these poor fans will be so happy lol, and we can actually get to the next JL faster than expected without rushing or making dumb decisions. IF you have a well received Aquaman, Shazam, WW (again), Bat, hopefully Flash by 2020, and you have both MOS2 and GLC released in 2021/2022, then you're really good to go for a JL2 in 2022/2023.