I mostly have 2 games like that in mind but there are many others too, especially if they're more focused on multiplayer - Anno 2070 and Heroes 6. I absolutely love the gameplay in those but the campaigns are just too short and have very little cutscenes and few story elements. Anno 2070 campaign for example only had 3 missions although they were divided into a more parts but since they all happened on the same maps and there wasnt exactly a lot to do, that hardly counts.
Don't get me wrong, I know it's usually a flaw in games with more sandbox gameplay but it doesn't have to be. For example Tropico 4 which was similar to Anno 2070 in many ways had a long story mode and 20 missions, some of them even quite difficult. Then Skyrim, even though from different genre also had hundreds of quests and many 10s of hours of quests chains on top of the main ones. It wasn't just about roaming around.
I recently picked up Heroes 6 since they released an expansion for it and it seems to have the same problem. Only 2 campaigns, both having like 3-4 missions and then a bunch of optional ones but you only have to complete one faction campaign to progress to the final missions and thats pretty much that.