Any way to make first city (capital) pre-defined?

I don't believe there is a way to do this, other than to go full scenario in which case you obviously get to place cities manually in a pre-defined map before it starts.

Well, you could edit this stuff in ElementalDefs:

        <!-- ** minimum materials yield at any tile with a grain yield ** -->
        <MinMaterialsTileYield>2.0</MinMaterialsTileYield>
        <!-- ** minimum combined tile yield at a tile needed for it to have a tile yield at all ** -->
        <MinValidTotalTileYield>6.0</MinValidTotalTileYield>

You could crank up the minimum material yields. Or you could up the minimum (bottom) so only particularly good tiles can be settled on to begin with. Or, perhaps, both.

Couldn't help but notice these while I was copy-pasting that bit of code:

        <StartingCityTileYield>TileYieldGrain,4</StartingCityTileYield>
        <StartingCityTileYield>TileYieldMaterials,3</StartingCityTileYield>

Given Heavenfall's answer these two things have got to be turned off, otherwise it's as simple as editing the two values.

 EDIT: You could try using the GameModifier ApplyToTile and see if you can get it to change tile yields. If you can it's as "simple" as finding a way to make it so when you hit the settle button as a sov you cast that spell concurrently with settling the city.

I didn't check the code for it, but you might be able to change the type of city your sovereign builds. In the cityimprovements file, you can change the city improvement path and such, so if sovereign creates CityHubCapital, which can be upgraded to CityHub2, and has a unique building that cost 0 labor, and gives 4-<citygrain> grain etc, the player will be able to, on the first turn, change his capital to a 4/4/2 or whatever city.