The tier list SHOULD be/IS determined by matchups, weighted by position in the tier list. (this sounds circular but I assure you it isn't).
The general brief definition of a tier list is "a list that ranks characters in order of tournament viability among players of equal skill level" or something similar. In general, the better characters are going to be more populous in tournament, both because people will usually pick characters that give them a better chance of winning, AND because those better characters will tend to rise to the later rounds on virtue of their strengths.
In short, a character's tournament viability is almost completely determined by his or her matchups with the top segment of the cast.
As far as Jiggs goes, I think the main thing to explain Jiggs' recent successes is a trait which I haven't heard discussed and will call "malleability". Jiggs' matchups aren't any better than that of either Falcon or Peach; all three of them are at a significant disadvantage vs 3 of the top 4 and are evenish with the last. Their matchups among the high tiers are all comparable too, I think. In an abstract situation where players are assumed equal skill and matchup experience, Jiggs would not be performing any better.
Jiggs however, because of how awkward he is to play against/all the gay things he can do/his strange properties (what KirbyKaze was saying earlier basically), allows whoever plays him to work around his disadvantages more than the other two characters. That is, differences in skill, style, or experience between players can help Jiggs more than it can help Falcon or Peach. Thus players like Mango and Hungrybox have been able to use Jiggs to incredibly high finishes.
Part of this I think is the fact that the anti-Peach and -Falcon metagames are much much stronger in general. Peach and Falcon have been played by top players for years and people generally have experience against them and know how to exploit them with top tiers. Jiggs hardly got any representation except for King who didn't play as much as other top players (until Mango).
As for Samus... well her top tier matchups are comparable (again, 3 unfavorable and 1 even), but her high tier matchups are worse overall than Falcon, Jiggs, or Peach.
Hell, if anything, isn't Ganon a bit more underrated than Samus is? >.>