I'm stuck in a predicament. I originally only had masculine and feminine, but I came up with a third gender, the inanimate/neuter. I don't entirely know how this new noun class could come into existence from a noun class binary, so it creates problems with how nouns in this gender concord with pronouns and suffixes.
Essentially I now have this (in order: masculine, feminine, inanimate, masculine, feminine, inanimate):

Every noun has a final vowel that determines its class (u = feminine, i = masculine, a = inanimate)
But I only have possessive suffixes and subject suffixes for masculine and feminine only:

These affixes are intended to be morphologically the oldest features, older than even the case system.
There are three possible ways for the two genders to split into three:

Possibility A is most sensible and elegant, especially if one could say the masculine is a reanalysis of animate suffixes combined with some i-colouring affix. But it would result in the problem of needing new masculine suffixes because the possessive and subject affixes would originally be animate and inanimate.
Possibility B can work by having inanimate/neuter nouns concord with feminine possessive and subject suffixes, but there isn't anything in the morphology that could suggest the feminine gender splitting into two. It would also mean that the possessive and subject affixes were originally masculine and feminine and now new inanimate suffixes must be created.
There's Possibility C where both genders split into animate and inanimate (so 4 genders) and the feminine and masculine inanimate nouns merge into one gender, but that still leads to the same issues as possibility B.
Now, I could just take the existing affixes and make versions where the vowel is <a>: (-ma, -man, -ta/-sa, -tan/-san, -ka, -kan), but that doesn't really make sense and it would create a lot of awkward asymmetry (when would you ever refer to an inanimate object with the second person?) and I don't really want to have a pyramid of gender distinctions (first person not distinguishing gender, 2nd person only distinguishing two, third person distinguishing three). So the solution is undesirable and maybe not even feasible. Making it so the suffixes don't make distinctions based on gender is also undesirable.