I am glad to see us another step closer to retcon.
I think I'd like the checklist to be more of an on/off switch system than a list of choices. I understand that wouldn't work for all of the lists, but it does for most of them. (examples will follow on each table.)
Basic options table. I like to see this, but it obviously needs more than one choice.
perhaps have this be either the level requirement choice or the skill power choice tied as the "foundation" choice. ex:
Foundation Choice wrote: Choose one of the following:
Basic (complete lv 11 quest) 1pt
Heroic (reach lv 20) 5pt
Super-heroic (reach level 50) 10pt
Items table, I like having a default choice that gets modified by the check boxes here:
Items wrote:Begin with all items (no point bonus), or choose one of the following:
 Gadgeteer access ("rebuild", aka pull, 10 items from your inventory each day.) +1
 Psion access (recall where you misplaced 5 items from your inventory each day) +2
 Elemental access (only the basics, just IotM access) +1
 Naturalist access ("who needs it?" no access to previous items) +5
The class name flavoring might confuse some people, I think it sounded appropriate. Alternately, Elemental access could be the ronin level and you could simply increase the point cost of gadget and psion to 2 and 3 respectively. Though, personally, I don't care for the ronin style.
Skills, I don't have much to change... though here's an example of the on/off switches:
Skills wrote:You'll have access to all your mastered skills, unless you choose otherwise:
 difficulty learning (non class skills cost 2x for each level) +2
 Amnesia (all previous skills turned off) +5
The on/off approach simplifies it a little and doesn't require you to check a box in each and every category if you choose not to... Also, If you limit the permed/mastered skills to only spending points on ones that are class specific, I think you'll be maxing out class level to easily and the cross class ones will be too weak to be much use. Therefore I changed it to having a higher cost for each level, though I know nothing about coding, so I am unaware of how much trouble that could be to create.
Consumables are the best example of simplified on/off switches. You wouldn't need to create the extra label for "oxegenarian".
Consumables wrote:You are on normal consumption, unless you choose otherwise:
 Decaf (no caffeine) +3
 Diet (no sugar) +2
 Naturally Hyper (+1 hour each night) -1
Drops it from 5 to 3 checkboxes (though one of them provides negative points) and you still have all th options that were available in the old list. Plus a couple new combinations, I suppose.
Sidekick is pretty much just a simple on/off switch if you only consider the permanent sidekick. I'd like to see the sidekick items involved with this choice as well.
Sidekicks wrote:Your sidekick will be with you through thick and thin, unless you tell him/her to get lost:
 Tragedy (Your sidekick decided to go study at the Cube again, re-convince him to join you at level 9) +2
 Anti-Social (no access to previous item sidekicks) +2
 Loner (no sidekicks at all) +5
Loner might be a bit under valued due to giving up all use of the sidekick slot, but it gives you an idea of what I'm
I'd also like to see a way to limit equipment slots. At the most basic it would be just turning off one or both of the accessory slots for maybe +2 each. At the most involved you could turn off any equipment slot, though that would probably involve much coding since you would need to adjust for certain equipment slots such as vehicle since you would still need to get places, perhaps you simply would not get any of the other powers beyond range for your vehicle. You could use the same effect for weapons and shirts/pants/suits, where the player gets the power boost, but not any added benefit/drawback, or you could write in equations with those slots that gives them extra power boosts as they level in those areas since they couldn't wear items in those slots. for example:
 Pacifist (no weapons: you lose all benefits from weapons other than their power) *or* (no weapons: You will get an increase to your attacks/damage based on your level since you cannot wield weapons "PACIFIST CRUSH!") *bonus points if you caught that reference
and the same can be done for clothing and vehicle slots. I think it would be a fun restriction to try, though I don't know how others would feel about it...
As for all the other posted ideas, I assume the comparisons were simply to benefit the community in giving examples for how they could combine their options for KoL style runs and that they will not be "preset" run options? Leaderboards I have never been terribly interested in, but the bonuses and prizes both look really good for what you have listed so far. Mystery prizes! YAY!