Gary Kubiak is a WCO guy who, like Shanahan, likes to pair that passing attack with Alex Gibbs' Zone Series rushing attack. WCO is very complex and specific in its calls which are very long since they tell the formation, where each eligible receiver lines up in it, shifts and motion and which route each runs.
If I'm not mistaken, when Manning was at Indy they used balanced formations with little motion. Since he has been at Denver, that has changed since the Broncos use unbalanced formations like Bunch and utilize motion with Z and H receivers.
The big difference between Kubiak's and Manning's offensive philosophy would be the latter's fondness of reading coverages and calling plays while the playclock is winding down. That practice necessitates a way of communicating at the LOS which is complex for those hearing the signals, but is much simpler than a WCO system.
IMO, in order for Kubiak and Manning to work together, the latter would need to surrender some autonomy and the former would need to allow a simplification of his system.
Whether or not Kubiak would favor a rushing attack which is a mix of angle blocking and zone steps, or if he would want to be strictly zone is another issue.
"Stultum est timere quod vitare non potes." ~ Publilius Syrus