I'll take my chances to show my personal main parings
But first the character of parings, but in a Owner/Pet (or companion) relationship
and
(Subspace Emissary helped)
with
and both
and
(The Master and their Pokémon)
and
(It is an Owner/Plant relationship, but Villager will take good care of Piranha Plant)
Viridi and
(Palutena's guidance, mush to Palutena's dismay)
Here is a surprising one I have thought of
and
(Inkling happened to discover Lugia perching on Moray Towers and she had a Pokeball, and hence, a new alliance was formed)
Basically any Pokémon with their companions, as long as they are trustworthy
Same thing applies to Steve/Alex and their pet dogs (wolves), cats, horses and parrots (amoung the other creatures in Minecraft)
Now the true OTP
x
(Brawl in the Family web comic helped, but they are both cute together)
x
(Common, but they are meant to be together)
x
(Same, with Brawl in the Family helping again)
x
(Cannon)
x
(Another common paring)
x Dixie Kong (If only Dixie was playable)
Link x Zelda (Common)
Popo x Nana (thanks to above, and they are back)
x Krystal (They trust their instincts)
x Fiora (Cannon)
Now for friend relationships (Best friends and such)
and
(Subspace emissary)
and
(They are very cute)
and
(Another planned out idea, they have teamed up against Mewtwo and both Incineroar and Lugia became allies)
and
(Warning, there could be a lot of puns involved with this alliance. However, Inkling may want be more then friends with Pit however)
To finish up with relative relationship (parents, kids, brothers, sisters and cousins)
and
(Father and children relationship)
and
(Brother relationship)
and
(Father and Daughter relationship)
and
(Mother and adaptive son relationship)
This is what I got for now