Some people are still committing the logical fallacy of trying to design a ruleset so that the "better player" wins. That is an ignorant exercise. I don't know how else I can say this.
The better player is the one that wins under whatever ruleset is constructed. It does not matter how many games are played - this remains true regardless. The ruleset is designed depending on what skills the TO deems valuable. And you don't, you DON'T, try to eliminate upsets, because by trying to claim that's what you're doing, you are also saying that there's no point in playing matches. If the better player wins every time, why play at all? We already know the results. Look, if I played Mango in 15,000 friendlies with items on and beat him every time (assume that he's trying his hardest), then lost to him three times in tournaments with no-items play, who's the better player?
The right answer: There's no such thing as a "better player" independent of ruleset. If you doubled the length of every golf hole in the world this second, the leaderboards would look a lot different. Same if you halved it. Lowering a bball hoop to 5 feet would drastically change the dynamics of that game, and would change what it would take to be a "better player."
(Don't go crazy on me - some players are obviously better than others, but that's judged on tournament results, which again goes back to rulesets. In the earliest days, everyone used to think that BTT and HRC guys would be the best players because they looked so crazy good, but then they lost all the time in tournaments and we realized that wasn't a good way to estimate skill. We didn't change our rules to play only BTT at tournaments because we thought the "better players" weren't winning. That's crazy talk.)
Bo3 and Bo5 are neither inherently good nor inherently bad rules. Both test your skill at Melee. Bo3 saves time, especially during matches that would simply change from 2-0s to 3-0s, which are 80% of matches in early rounds. Thus, players don't waste energy on lower-level matches when they could be saving it for high-level play later in the tournament, and the quality of match play remains higher at the end. However, it does allow for 5-10% more "upsets," usually between the players who are so close in skill that you shouldn't call it an upset anyway. Bo5 allows players who are close in skill level to display more of the depth of their game knowledge, which is also great. However, Bo5 doesn't show any depth of game knowledge when one player is so clearly superior that he barely has to try, which is true even for some 5th vs. 9th place matches, and if that's the case then it's just a waste of time. That's it. That's the entire argument. You can do either one.
The reason why it's typically Bo3 early and Bo5 late is because most matches in seeded tournament play are not very close until the late rounds, rendering a Bo5 a waste of time and energy. However, later it makes more sense to test this to a larger degree between players who are assumedly closer.
EDIT: I'll add that in some tournaments, there's no point in even having Bo5 at the end. If Mango and the 17th best player in the country are the best players at a tournament and playing a finals set, he's likely going to get rocked no matter how long it is and Bo5 shows nothing more than a B03 would. Conversely, at FC3, I'm pretty sure we ran the whole bracket as a best of 5 because the depth was so ridiculous.