I don't mind Rinnosuke being that tall compared to the Gensokyo girls. In fact, his height is just perfect for Keine. When she hugs him, her head is near his chest, meaning she can hear his heart beat.
On the contrary, on MachThreeSlug's linked picture, Marisa's small size has its advantages from a certain point of view, seeing as she can give head to Rinnosuke while still standing.