I read your series today and I really liked them. Your opinions are well supported, and your analysis covers each keyword from many different aspects in a broad view.
I have one correction to make though. Suspend wasn't the first ability to use the exile zone in a way that no other card could, imprint in Mirrodin block did it first (albeit in an unexciting and not very memorable way). This mechanic still has quite a lot of untapped design space.
I don't have an idea what the first keyword would be. Trample is one of the most beloved mechanics of all time, that plays well and has history. However, it's not very innovative - many attacking/blocking mechanic have been made alongside it from the very beginning, and it's not as resonant as flying.
OTOH I definitely know what will make the worst ten keywords of all time: Shroud!
I'd cut Kor SKyfisher. If it is only between the two, Paladin is my cut. I do think Remorseful Cleric is better than both suggested cuts, but not by much. If your cube has few grave-centric decks, I'd not bother adding it.
Force >> Negate > Spell Pierce. I was hesitant to add Force, but it proved to be powerful.
Hagra Bite > Fatal Push > Bone Shredder. Bite's performance is speculation of course.
Declaration >> Prison Realm
I've never played Aphemia, but I believe she is worse. Being able to block is an upside, but not trading with a thopter token is a more important one for aggro decks, which are the only type of deck to be interested in such a card. In enchantment themed cubes things might be different, but I believe it is safe to ignore the triggered ability in the typical cube setting.
Lich is the most powerful of the bunch. The rest is context-dependent. LDM is the most self-contained of the bunch. LD is the best build-around and creates better stories. Whisperer plays double duty in reanimation lists. I'd personally cut Whisperer, it was disappointing in midrange lists without graveyard synergies.
Spiritkeeper > Apparition. Spiritkeeper is one of the better tools white-based aggro decks have against mass removals, but it is also good in token decks, Recurring Nightmare, and so on. I believe Apparition's competition is more with Oblivion Ring and its ilk, as it is a card you would likely keep in hand in the search for a good target to exile instead of casting it on curve.
Mirror Mage is better. I've always wanted to kick Jace
I agree with you this card is stronger than Boon of the Wish Giver, just not with your argument. SGR will compete for deck slots with lands, and can replace a basic island. Boon is not a consistent mana source, and therefore replaces a spell in deck construction. Boon just faces stronger competition, so it has a higher bar to hold up to.
I see SGR as a card I will side out against aggressive decks. The spell is very expensive and does nothing to the board and paying 3 life is very risky. However, Castle Vantress is not a card I'd be sad to see go at all. I'll follow results with SGR closely to see if I should make this swap.
Confluence > Command > Inscription
Command > Inscription
Meren > Deed
Wreckage > Catastrophe
This is very far from my experience with cycling. I often cycle to find an answer/blocker, or just to use mana at an end of turn if I have one free because I didn't counter something, and/or do not expect the spell side to be more relevant than a random card at this point in time.
The red one cannot go to face.
It cannot exile tokens
Gideon of the Trials is almost a creature. Eldrazi Displacer is quite fun and good enough to be competitive if players draft around it. Ranger-Captain of Eos is white card advantage and is solid value.
Thirst > Push > Eat
Advocate > Protector
Karplusan > Grove
The Scarab God is very strong
Mirran Crusader by quite a bit. Crusader doesn't require another creature to beat for four, has partial evasion and is harder to remove. Granting another creature double strike is nice, but is also risky as the Paladin can be easily removed mid-combat. Crusader is the card you want to buff and equip.
I don't think being locked into one color of mana is a deal-breaker. I am very rarely keeping hands with a single colored mana source anyway. Always coming into play untapped is key, especially in guilds like Boros that feature one drops in both colors.