Pepperony was designed as a ship going into the story; Pepper was introduced as a partner to the superhero lead and the romance was assumed to follow. RDJ probably had some say but it worked because it was designed to work and cast with a top tier actress.
Cap and Widow were reintroduced in TWS as mission partners and their romantic compatibility in TWS was teased, albiet with the designated future cannon love interest in the background. What TPTB may have not anticipated is that CapTasha was maybe a little more intriguing as a romantic pair to some fans (because CE and BW are great together, mostly) than the possibility of Staron. (Not to mention the lingering ghost ship Steggy.)
Do they even care what the fans think? There must be a intern that monitors this kind of on-line chatter...
I say, ship whomever you like. Marvel's track record proves that they will never deliver in a way that matches what the fans want because fan imagination can be fairly insatiable. It's all good.