Could this be a better question?
Of course Marner has proven to not have been a bad selection, he's been fantastic. However...rumors were strong that Hunter and Babcock were at a disagreement on the Marner selection, apparently Babcock really wanted a big defensemen (rumoured to be Hanifin).
Hunter perhaps played it safe and went with the known commodity in Marner, someone he knew would at least be a impact player in the NHL. Or maybe some will argue, he made the choice with the idea that Marner will be the best player/period at #5. Lets not forget that their were rumours that a few teams were interested in trading up to acquire Hanifin, obviously one being Columbus. I don't recall hearing about teams wanting to trade up for Marner. Heck, Columbus almost traded 3 2nd rnd picks, just to move up and draft Hanifin at 4.
In knowing the value of a top pairing defenseman in the NHL, and the cost to acquire one... ex. #1 overall pick Hall, for Larsson (can we use Chia trades to set standards?), and the #1 Centre with size in Ryan Johansen for the unproven young defenseman Seth Jones (who obviously was highly touted)...
Was going with a small winger the right choice?
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Hunter more than anyone understands the value of players by position and that #1C and Top pairing Dmen >>> Wingers as Vital/Key team building blocks.
When Hunter drafted Marner, he also premised and defended his pick by suggesting Marner (a winger in OHL) would be a future C in the NHL and would be developed into one down the road. Also Marner's old brother (Christopher) had a late growth spurt shooting him from 5-11 to 6-3 in size at age 18-19, and Hunter crossed his fingers telling Leaf Nation that he hoped the same would happen for Mitch.
So it was a calculated gamble by Hunter, banking on a position change and a potential late growth spurt by Marner moving him to C position and hoping for 6-2/6-3 in size. As we find out now that neither of those Hunter gambles came to fruition and so Leafs ended up with a small highly skilled winger as a top 5 pick in a strong draft class. So drafting a non vital building block positional player will be questioned no doubt in that regard .... but had Hunter's calculated risk actually happened and Marner seen that 4" growth spurt and successfully transitioned to C position then he would had a player to potentially rival Eichel #2 OA as a big #1C and Hunter would have looked like a genius.
You're 100% correct Babcock wanted a big Dman as a building block with the Leafs pick either by drafting one at #4 or trading back to #8OA and taking one there. Whether there will be any Coach vs Marner long term impact in terms of resentment or regrets that he didn't get the player he wanted at the draft remains to be seen. As we have seen the coach does prefer size in his players and ones that can win puck battles and use that size and drive possession.
At present Marner is being used as a 3rd line RW to drive Leafs #3 line offensively (with JVR and Bozak) and giving the Leafs a mismatch QofC against the oppositions 3rd and 4th lines on skill to allow them statistically to provide secondary attack behind Leafs top 2 lines on Matthews and Kadri. Leafs depth at forward is now a team strength and Marner drives that by the coach usage and matchups.
PS. However Hunter and the Leafs lucked out in the big picture, because Leafs successfully tanked and got their big #1C Matthews the following year, and also Nylander (a winger) taken before Hunter arrived also potentially is viewed as a centre down the road. So now having Marner a highly skilled winger is not a bad thing as other pieces fell into place for the Leafs. So this could all work out in the long run if the Leafs successfully win a Cup down the road.