1-3-1 is standard across the entire NHL. It's really not the issue.
I think the bigger crime is not putting Spezza on the top one. You could also argue that Sandin should be swapped with Rielly.
My take:
Tavares
Matthews - Nylander - Spezza
Rielly
Ritchie
Engvall - Bunting - Marner
Sandin
Spezza is a big shooting threat and he's a fantastic puck handler. You can put him in the bumper spot too. I think Rielly has been far too hesitant in shooting or using lanes properly on the PP1. He's relying on distributing to Matthews or Marner far too often but without Marner, I think Rielly can dish to Spezza who can actually be a scoring one-timer threat instead of passing it to Marner where everyone knows what he's going to do (curl, carry, wrister blocked -- out)
Marner has struggled immensely on the PP but maybe giving him less minutes on it and a different set of players to play with might kind of jar something loose. Let him be the primary forward on it. It would be similar to when Nylander was on the 2nd PP to let him handle that unit and it kinda worked.
Could swap Sandin and Rielly but I'd rather give Sandin the horns of the PP2 with Marner since it would miss a bit of a shooting threat.
Just because it is the standard, doesn't mean we have to use it.
Marner simply doesn't work on a 1-3-1. He doesn't have the shot, no matter if you put him in the bumper or on the right wall. The only place he may work is in Rielly's spot, but then you have to either take a defenseman off of the PP, because neither are going to work along the wall nor in the bumper spot themselves.
Alternatively, if you use a 2-2-1, like the Marlies have used many times (including with pure playmakers like Bracco), or a 3-1-1, like the Swedes used at the U20's when Sandin was on the team, then you can have a guy like Marner act as a playmaker along the wall and still have many of the benefits of the 1-3-1 and 2-2-1, but I think you need a strong RH one-timer on the other end of the ice (Spezza or Nylander), a big body out front (Ritchie), and a really strong bumper (Tavares). I think you also want Sandin's one-timer as well up top, since you are running things from the boards instead of purely on the blueline.
Bunting
Matthews-Engvall-Spezza
Rielly
Ritchie
Tavares
Nylander-Sandin-Marner
Ideally, I think it would have been better to swap Tavares and Engvall so you can have Tavares there for tips on the Rielly unit, but Engvall will need to learn that tips (both from the wings, especially Spezza, and from Rielly) and rebounds are going to be how he scores a lot of his goals, and that he will get a ton of excellent slot chances to bury goals.