It's likely because Dion's defensive play is not his natural instinct.
This suggestion is made by you. Let me ask you, who are you? The fact that he goes up against top competition which is NOT conventional suggests that his defensive game must be elite. Seeing that Keith - Seabrooke are not used in a shut down role tells us that he's pretty competitive.
Yes, Sutter is included in the article you linked, but that's not what you quoted from the article.
As anyone back then noted, he played an intelligent game keeping plays simple and being reliable on both ends. Most who are familiar with him wouldn't suggest that he some sort of prototypical PMD. He isn't.
As I said above, Dion's play this year is not really his style. He is at his best when he's making an impact by making big hits and taking offensive chances. Give him a true shut-down defender beside him and let him run wild.
Dion had a "true" shut down defenceman in Regher, and let me tell you, it looked atrocious. In addition, we had a mighty different playing style from Calgary. Their team was a low tempo, tight-checking, and LOW scoring team. Much like Boston, you can get away without a protypical puck mover. In fact, they depended so heavily on Iginla and Phaneuf to drive offence, you could afford to throw a bunch of grinders around them. Seeing that we have Kessel ( or JVR) as our top forward(s) and not Sittler ( who played a lot like Iginla), that just isn't possible. .
On the Leafs, we have high tempo, counterattack playing style. We don't play a tight-checking game all through, but we can collapse well into our zone, and we're able to shut down top lines. The truth is, our defensive zone game is actually very effective. The problem is, we lack an
offensive top pairing of the Keith -Seabrook variety to make better use of the puck. Gardiner, right now, isn't that good enough while Franson needs to be sheltered. Rielly is too green as well, I am not sure if he'll offensively break out in a Phaneuf-esque manner.
As I said, Phaneuf would do better with a Jonas Brodin or Ryan McDonagh type of puck mover. Someone that can control the tempo of the game and can be very creative with the puck. In other words, an extremely high IQ type on the DEFENSIVE end of the ice. I could see Phaneuf doing a lot better in that regard, because he's really more of a defensive defenceman with a good shot. Actually, let me be condescending: watch him play and it gets very obvious. He isn't a prototypical quarterback and should NOT be used in that manner.