I stayed awhile and listened.
I don't like the idea of combining secondaries. Instead, I think it should be a straight-up reroll but with at least the same number of secondaries as the inputs with a chance to get one more. The recipe would require two mods, maybe an Omega mat and some credits. The first mod is the one being rerolled and is guaranteed to keep the dots and minimum number of secondaries but the secondaries get rerolled. The second mod is a sacrificial template and must be the same shape but may be any number of dots or secondaries. The primary stat of the template will then get imprinted onto the first mod, guaranteeing that primary stat shows up on the reroll.
This allows you some degree of control over what you get and gives you a way to get rid of those low-dot mods you have no other use for while also maintaining the randomness that this game seems to love so much. Plus, almost every transmogrification recipe on the D2 cube involves a random roll of stats so this would keep that theme too.