Okay - I was a little busy, but after looking over your Series (and each card), here's what I have to say:
I love it. Well, if only the concept.
Some of your ideas simply 'take' from old mechanics in-game based off of either weapons, spells, or creature abilities, which makes each of them on different power levels from one another (which is hard when you try to 'balance' the ideas of a Series, but I know you tried). I'm going to give you a small 'summary' of how I feel about each rune, excluding the weapon itself, because I feel that it could be considered the first 'Other' rare that would simply 'generate' a Rune Spell in your hand based off of your mark.
That said, these work well with the Other permanents (the weak weapons like Dirk, Long Sword, and Gavel), because of the free cost it takes to summon those (and change them into your desired 'weapon' with an expensive cost).
Aether: The immortality effect is a little bit limited, and feels weird. Assuming the player wants the creature to be constantly immortalized, then the Phase effect is weak for several reasons. First off, a creature with an important ability (Druids, Firefly Queen, Anubis, etc.) probably wouldn't be targeted by this ability, because their abilities are generally much more significant than a 1-turn immortality usage (so only strong creatures would benefit). Secondly, since none of Aether's creatures can be immortalized (since they already are or die anyway - see Spark), this makes this card only usable for duo's or elements that splash
quanta. Finally, because it only lasts for a turn (and it costs 1
quanta each time), the upkeep is a constant strain on the creature, compared to Quintessence, where it only takes 3
quanta and lasts for the entire game (unless the creature is killed by Fire Shield or Thorn Carapace).
If you're going to keep that ability as is, the immortality effect might as well be a 'triggered' ability that keeps the creature immortalized as long as you have
quanta - the only benefit I see is the situation above, where you want to rewind your immortalized creature that's poisoned or about to die.
Likewise, having lobotomize is a card that works well against creature with abilities or momentum, but aside from that, it seems to be too limited.
Air: Very powerful (if not completely overpowered) for both abilities. Having a line of creatures with Dive (see dragons and other strong creatures) will be devastating against your opponent, and having ample permanent control with Sniper (assuming you have the
quanta for it) would be pretty frustrating to deal with. Dive generally costs 2
quanta for a reason - with only 1
quanta, a deadly creature (say, a Momentum-affected Ruby Dragon), would finish off opponents easy as long as you had an
mark.
Darkness: See above about my issue with the 'gaining an ability that requires an 'on-use' effect that last for one turn limitation'. It is technically better than Liquid Shadow if you don't have any healing abilities for the creature, but the only benefit would again, be mainly from tougher creatures that have a lot ATK power (or ones that have no abilities what so ever).
The devourer effect is pretty strong as is - does this stack on a permanent with multiple 'layers'? (Bone Wall, pillars, permanents) If so, then Darkness would have the most ridiculously easy way of getting Darkness quanta - multiple Darkness pillars, devourers, and then having this on your permanents - unless the opponent has massive ways of gaining quanta or can destroy the effect, they'll be sucked dry even worse than black hole/quicksand/devourer combinations.
Death: The creature effect is somewhat balanced, but still pretty devastating with the right (durable) creature to use it with. The permanent effect, however, is downright broken - with the recent additions and changes to poison, this card would tip the scale of every deck desiring some form of Purify in one way or another.
Earth: Harden combines well with a protected Gravity Shield, and makes the synergy better than with Auburn Nymphs. The 'Resist' effect is interesting though.
Entropy: Chaos Power (or Chaos Seed) repetition/abuse is inevitable. Suppose you have a Discord with the Chaos Rune effect - with a pure mono, you can play a Micro Abomination (cheap Entropy creature), use Butterfly Effect on it (giving it the power to destroy the opponent's permanents), then use the Chaos Power spell on it (increasing its attack and HP). Rinse and repeat that with other abominations (who may instead get the 'Scramble' effect), and you have a pure-mono Entropy that has multiple 'discords' on the field, a reliable way of PC, and massive damage potential.
Fire: ...this is somewhat balanced I suppose, but it does seem somewhat weird to have a permanent 'destroy itself' for a boost of fire quanta.
Gravity: A more expensive momentum makes this card less fun to use on creatures (unless you plan on using momentum on nearly every creature on your field to ensure that they bypass shields), and the Gravity Pull effect on a permanent for repeated use just doesn't sit right with me.
Life: Easily exploitable with having different pillars in addition to a reliable source of
quanta. You can practically have Shards of Gratitude in your deck without needing a single one (just target a off-element pillar and bam, you get regeneration with quanta production).
The creature effect however, does combat nicely against Infection statuses, which is something I approve of. It's still powerful though if used correctly (say, on a Elite Armagio or Liquid Shadowed creature).
Light: The permanent effect almost seemed useless, but I suppose it can work in some decks that want to exploit Hope (a micro abomination/fractal spam with bioluminescence?). The creature ability is decent, but would make angels fairly useless if you can cast this on Light Dragon or high-HP creature.
Overall though, the Rune effects for Light are probably the weakest out of all of the elements.
Time: Major issues with this one.
Deja Vu for an ability would give Time a massive advantage over Aether's Twin Universe spell, assuming the creature doesn't get killed, rewound, delayed/frozen, or lobotomized. The only downfall is the fact that the creature would lose its starting ability, but if done correctly, Deja Vu would be a near show stopper and would make rush decks all the more devastating - I'd say that giving any creature the ability to 'Deja Vu' is too strong, and would make the synergy between Aether and Time almost impossible to stop (say, giving Deja Vu to a Silurian Dragon, using TU on it, and immortalizing one or both of them = 40 damage right there). The expensive cost probably doesn't benefit much from it.
Constant rewind would give players a new incentive to instead use this in their rainbows for three reasons. 1) Unless they're facing a False God with heavy pillar control, you can probably use the Time Rune on a stack of Quantum Pillars and get a relatively easier way of preventing deckout (the opponent that would try to destroy your pillars would have a hard time doing so, unless they spam earthquakes/quicksands); 2) Frees up the weapon slot for Pulverizer or another permanent to assist with CC, PC, or whatnot, and 3) allows the player the option to not have to worry about countering Permanent control from the A.I. so much, because unless the whole stack is destroyed, then they'll still have the Rewind ability.
I love time cards, but you might have been pushing your luck with this one. ^^;;
Water: Both abilities are freeze, which turns the creature into an Arctic Squid that can survive Flooding. It's okay I suppose in a Water-Death duo with high amounts of CC (to help stack Bonewall counters), but aside from that, freezing everything is still pretty limited.
Anyway - I think that the best card from here is probably the Rune Sword itself (generating 'runes' for whatever reason). The elemental cards range from being massively broken (in mechanic, cost, etc.) to somewhat balanced, but I think that having entirely new mechanics will give your Series a much more fresher look from observers. It's important to note that, of course, this is all just theorycrafting and my opinion about it, so take what suits you best and fix/add/remove/leave parts of your idea as you see fit.
...(This is the only 'elemental' series so far that I've thoroughly enjoyed, since the idea of 'Runes' seems similar, but not exactly like the Alchemy spells that was implemented earlier)
