When have they played 11 games together? From what I noticed, for whatever reason, it takes Matthews more than the average player's time to build chemistry with his line mates.
I don't know where you are getting this from, but statistics show that Matthews has had almost instant chemistry with everybody (except Marner and Komorov). Nylander, Hyman, Kadri, Kapanen, Johnsson, Leivo, Tavares etc.
And to your other points, Matthews Nylander have not consistently produced well together in meaningful games and are always split up.
This is not true. Nylander and Matthews have been consistent playing with each other before this year. They played well together in the series against Washington (where they were not split up). They were split up eventually against Boston to get Nylander away from Chara. Chara shut down everyone that year (which includes Kucherov and Stamkos who he completely shut down in the next round) and this year (when Marner and Tavares could not produce at all against him).
If Marner is playing with Tavares that easily makes them a shut down line that plays against top opposition.
I am not sure you understand what a shut down line is. Kadri centred a shut down line last year, but Matthews played against top lines just as often. Few teams have a shut down line. Tavares was not used as a shut down line this year. McDavid and MacKinnon are not used as shut down lines. Most teams just play best against best, with the intention being to outscore their opponents, and not generally a focus on shutting them down.
I showed a couple weeks ago that Matthews went up against their opponent's best forwards almost as often as Tavares did this year, and he went up against their opponent's top Ds (which is what most coaches focus on) almost as often as Tavares as well.
I think the culture has to change, Matthews has got to start being the guy but he never will be with Nylander beside him defensively.
Matthews was the guy just the season before - while playing with Nylander. Remember that? When the Leafs only allowed 2.00 GA/60 at 5v5 with Matthews on the ice and scored 4.07 GF/60 while going up against QoC in the 98th percentile (with Tavares this year they were 3.97 GF/60 and 2.68 GA/60). This year Matthews got the crap end of the stick. He played with linemates who were hopeless at controlled exits and got hemmed into their own zone. That doesn't happen with Nylander, and is why the two of them should be together. The Tavares/Marner/Hyman line works because both Marner and Tavares are really strong at zone exits and entries and Hyman is good at creating chaos in the opposing zone stopping the opponents from getting controlled exits. The Matthews and two of Marleau/Kapanen/Johnsson line did not work because with the exception of Matthews the other three suck at zone exists and zone entries, which allowed teams to solely focus on Matthews. Nylander is one of the best at zone exits and entries, and while people think that he is poor defensively - I will take a player who gets the puck out with control better than almost anyone else any day. And incidentally over the last three seasons Nylander's 5v5 GA/60 is lower than any other Leafs' forward.