The "what civ", "what map", "what size" and "what level" options are carried through from non-mod games - start a non-mod game, pick your options (if you do this from the advanced setup screen, select back and then start game) and play one turn.
Exit the non-mod game, now when you go into the mod game setup those options will be pre-set.
If you want to save things like "New Random Seed" that can only be done by "hacking" an XML file. Locate "C:\Program Files (x86)\Steam\SteamApps\common\sid meier's civilization v\assets\Gameplay\XML\GameInfo\CIV5GameOptions.xml " and edit it with a plain text editor (Notepad is good) and set Default to true for each option you want checked, eg
Code:
<Row>
<Type>GAMEOPTION_NEW_RANDOM_SEED</Type>
<Description>TXT_KEY_GAME_OPTION_NEW_RANDOM_SEED</Description>
<Help>TXT_KEY_GAME_OPTION_NEW_RANDOM_SEED_HELP</Help>
<Default>true</Default>
</Row>
If you want to change the default resource allocations you can only do that in the map scripts, or in the MapGenerator file
Locate "C:\Program Files (x86)\Steam\SteamApps\common\sid meier's civilization v\assets\Gameplay\Lua\MapGenerator.lua" and edit it with a plain text editor
Find the following block of code and change the DefaultValue to what you want - Abundant is 3
Code:
local resources = {
Name = "TXT_KEY_MAP_OPTION_RESOURCES",
Values = {
"TXT_KEY_MAP_OPTION_SPARSE",
"TXT_KEY_MAP_OPTION_STANDARD",
"TXT_KEY_MAP_OPTION_ABUNDANT",
"TXT_KEY_MAP_OPTION_LEGENDARY_START",
"TXT_KEY_MAP_OPTION_STRATEGIC_BALANCE",
"TXT_KEY_MAP_OPTION_RANDOM",
},
DefaultValue = 3,
SortPriority = -95,
};
The changes in the xml and lua files will be lost when Civ updates itself (or you revalidate the game), so make a note of what you change so you can put it back after an update!
Yes it's a PITA having to edit files, but better than setting them for every game.
(And there are good reasons why mod selections arn't saved from game to game to do with "what if I was playing Civ X but that mod is disabled in the next game I play")
HTH
W