I'll comment on what I can since I said I would and forgot about it til now.
GAMEOPTION_AGGRESSIVE_AI - damages AI
Yes, but its a huge favorite and it might not be as damaging as it was. The settler inhibition it created was pretty brutal. It's not as bad now but the problem that still remains is that this extra aggression can tend to unbalance the AI's approach to the game and lead to an early determination of what player wins because they're constantly going hard for a military edge and any way to use it. This means they ignore building up their empire and possibly outteching opponents before trying to engage them. This might be an option that in the future could be retooled to be more useful if it allows the AI to be a bit more intelligent and less brutish. I've never had the time to fully investigate but figure it should be at some point.
GAMEOPTION_ONE_CITY_CHALLENGE - mod is too full of stuff for this option
Again, some people like it still and if I'm not mistaken, Toffer was doing his darnedest to make it functional, even if it will always write off some aspects of the mod. I mean, it always HAS written off a lot of the game before so that's not exactly a total killer for the option to not have access to some buildings. And if we write some exception rules for those buildings/techs that are critical if this option is on, we may be able to make it playable still.
GAMEOPTION_NEW_RANDOM_SEED - causes problems with debugging
Yes, but when we have a truly stable platform, this may not be so bad to re-enable someday. When we turned it off, it was because we were really crashing a LOT and needing the reports to correct that. With further devel we'll probably start having more again too, but I like leaving it here for the more advanced player who understands the consequences of it and is willing to use it anyhow.
GAMEOPTION_LOCK_MODS - ?
Vanilla option that I really don't understand but wouldn't dare to remove in full.
GAMEOPTION_NO_GOODY_HUTS - ?
We took this invisible because who really wants this? And we have a lot of options as it is and are trying to keep the list shorter if we can. However, if someone really doesn't like them, I don't mind them being able to go into the xml and turn it off easily enough.
GAMEOPTION_RUTHLESS_AI - damages AI - same as the aggressive one but another layer of stuff. Not sure what the intended difference was except to be something of an inbetween setting I think.
GAMEOPTION_NO_FUTURE -
I'd really prefer to see this become a drop selection on all map scripts what the last era they player wants to allow in the game is so killing this option may be ok BUT it also would be a faster one to get debugged and up and running in the meantime so that's why we've left it there. It's very bugged IIRC though.
GAMEOPTION_STRENGTH_IN_NUMBERS - WIP
Yes, WIP and under some scrutiny at the moment...
GAMEOPTION_SCALE_CITY_LIMITS - ?
I really don't know what this is supposed to do exactly but if it's simply made a part of the other city limit happiness penalties option then it can probably be removed.
GAMEOPTION_LS612_TRAITS
I think we gotta just leave this here for now, though Joe's suggest about making it a modmod may work instead of having it as an option.
GAMEOPTION_HEART_OF_WAR - WIP
GAMEOPTION_BATTLEWORN - WIP
GAMEOPTION_UPRANGE - WIP
GAMEOPTION_EQUIPMENT - WIP
Yeah all works in process and TBH, Heart of War is heavy on my mind as something that may be just about ready to go as soon as the unit review is finished. Battleworn as well is right there potentially if I can work out some of the odds stuff that goes with it. Uprange and equipment might be a little bit more of a wait but a lot of platform stuff has gone into uprange progress, particularly with a few things I will be including in the unit review.
GAMEOPTION_MAXIMUM_POPULATION - ?
I think this is something DH was considering working on and thus it was made an option to work with for that project.
GAMEOPTION_ONGOING_TRAINING - WIP
Yeah, and another I'd LOVE to get some progress on that the unit review is going to help me to do much easier.
GAMEOPTION_NIGHTMARE_MODE - was changed to be normal handicap, removed in savebreaking branch
This could be removed if we've set it up as an extra difficulty and all the challenges in doing so have been overcome. I'm not sure where we are with that.
GAMEOPTION_OUTBREAKS_AND_AFFLICTIONS - WIP
I'm very passionate about getting this done but want to make sure the unit review is in place first and all current property unit needs are filled before pushing forward further here.
Those options are hidden and enabled for various reasons (It seems like shouldn't be optional).
GAMEOPTION_MOUNTAINS - can build mountain mines, removed in savebreaking branch (now always active here)
I kinda figured DH refused to let this go...
GAMEOPTION_ASSIMILATION - allows assimilating other continental cultures - removed in savebreaking branch (now always active here)
I'd like to think that the Ideas project will obsolete this when it comes.
GAMEOPTION_ECOLOGICAL_ANIMALS - few animal units need this option - removed in savebreaking branch (now always active here)
DH's option and I'm not entirely sure what it's for, even though he's tried to explain a few times I think.