Now hear me out on this one.
Everybody talks about who the best waifu is, but you know what's better than one waifu? Two. (Three technically, but that's spoiler territory...) I'm talking Pyra/Mythra here, not only because of voluptuous bodies, large breasts and more curves than a race car track, but also because of the added benefits.
You get a sick ass Flame/Light sword and a Mech! Does Samus give you a sword? Does Peach give you a sword or a Mech? Nope. All Peach can cook is cake, Pyra can cook meals good enough to increase your stats! Samus isn't gonna let you use her power suit, but Pyra/Mythra can shield you during combat while you fuck up shit like the alphamale you deserve to be if you choose these two as the true waifu.
Need extra firepower or travel? Have Mythra call down Siren and you've got a freakin Gundam to fly everywhere! Who's gonna start shit with you if you're flying a Mech places? Nobody. That's who.
Also the sex is probably banging. But you gotta have the stamina to please both of them. What? You thought having a waifu is easy? Let alone Two? Nah-Nah-Nah, you gotta provide some loving in return, keep em satisfied.
In conclusion, Pyra/Mythra best.