Historically, Marines are soldiers who specialize in amphibious attacks, are commanded by naval officers, never in any nation has there been a case in which a unit of Marines came under the command of an Army officer, at least that I know of.
Yes, the Americans did not actually use the Marines in Europe, since they were largely using their Marines In the theater of the pacific.
The only two nations to make extensive use of Marines were the Japs and the Yankees. The British seem to have used them on rare occasions. In the end, I don't think it's good the generic way they portrayed this unit so important.
I find it odd that Marines are army units instead of Navy units. Wouldn't that be the case of a mistake made by the developers?
I suggest to change this and put the Marines as navy units that would be commanded exclusively by commanders that have the Naval Invasion ability.
So from what you have been saying there is no way to change, as far as the objective is to try to simplify as much as possible, even if this dislikes a part of the consumers.