If you don't like your starting equipment, you can open the sovereign's XML file with an editor or even just Notepad and change things around.
It is also possible to mod items in for customisation:
Copy an entry from CoreItems.xml/CoreWeapons.xml/CoreArmor.xml and paste into a new file. For example, the Amulet of Flames starts with this:
and ends with this:
You'll want to use a different internal name (what's in the quotes above!) to differentiate it from the item you copied.
To make an item available for sovereign creation, add/change this tag to the item:
If you want to charge one point for adding an item, use this tag:
Finally, you're going to want to add or change this so that your rank and file units don't have access to it:
I know that modding isn't for the faint of heart, but you'll know (having sunk 300 hours into it) what you would like to see added, so it's a lot quicker and easier for you to do it.