Hey InertialMage,

Unfortunately, splicing a population several times is not possible, except with some black magic with a quest which replaces the population with a similar population which can be spliced because it's not the same but its visual/title/description is the same blah blah...

Modifying the cost (number of populations required) of a splice is not possible yet: it involves modifying the Registry (which is something I haven't seen in public mods, it's fairly easy, but I'm not very sure myself how it works in details).

What you would have to do is override the formula "AssimilationThresholdFormula" which says how many populations are needed for each splice:

<AssimilationThresholdFormula>2 + $(AssimilatedPopulationsCount) * 2</AssimilationThresholdFormula>

The issue is that this formula does not have the Empire as a variable (only the number of assimilated populations), and thus cannot use any kind of "Splice cost reduction" property that could be found on the empire.

I'm going to add the empire as a variable, it won't be used in the vanilla game but you'll be able to use it after the next update.

Finally, upgrading the major population is possible:

You'd have to create a new StarSystemImprovement (built on system) or EmpireImprovement (active as soon as a Technology is unlocked) and have its SimulationDescriptors affect properties on populations with the tag MajorPopulation.

This is an example of a SimulationDescriptor you could have on an improvement, which increases the science per population on your major population only:

<SimulationDescriptor Name="ExampleMoreSciencePerPop" Type="ExampleMoreSciencePerPop">
    <Modifier TargetProperty="BonusPopulationScience" Operation="Addition" Value="1" Path="./ClassStarSystem/ClassPlanet/ClassPopulationPlanet,PopulationMajor"/>
</SimulationDescriptor>