My thoughts:
If the matchup is indeed in Pit's favor, it would be no higher than 60-40.
CQC
I think there's no doubt that Pit has better close-range abilities than Samus. Especially since he has swords. Though with well spacing, it seems difficult for Pit to land a KO move on Samus (IMO). It also seems that Samus is better at linking attacks together than Pit, but... maybe that's just because us Samus mains are used to comboing. =P
Because Pit has swords, I think that Samus' Ftilt is a major key because of it's range and speed. I used more Ftilt in those matches than what I normally would. But for the sake of priority, I believe Pit has the advantage in CQC.
Ranged
This is a close one. We just confirmed that Zair can indeed eat Pit's Arrows... though it's incredibly hard to actually do that. And Pit's Shield can reflect Samus' Zair. I laughed at that one. xD
Pit doesn't have nearly as much distance application as Samus has, but he still has one thing over her--Speed. His arrows come out faster than her missiles and beams, which can be pretty annoying. I personally think that ranged game is slightly in Samus' favor. Just slightly.
This matchup is pretty difficult for Samus. It's definitely a tough one for her, but I believe there's worse that she has to deal with. (Falco, Dedede, ect.) It's like a Snake matchup. It might seem in Samus' favor first, but if the Snake knows how to handle the Samus, it's in his favor.