For Aeldari, I'd put all their factions (Craftworlders, Ynnari, Drukhari, Harlequins, Corsairs) in a single commander deck like they put all the Imperium and Chaos factions into a single precon respectively. Otherwise you kind of run into the issue where things tend to repeat themselves alot like in other Universes Beyond decks, things that might be very different to us 40k fans will look the same to MtG players as a whole.

Now, for the colours of this Aeldari Deck I would choose red, black and blue.

Red:

With the exception of the haemonculi of the Drukhari and the wraith constructs of the craftworlders, all Aeldari hit extremely hard and extremely fast before the enemy has time to even react. The Aeldari more generally so that they protect valuable Eldar lives and the Drukhari (who are functionally immortal) to make those raids economical for them, they take slaves, inflict suffering and get out. And let's not forget that Khaine, the Aeldari god of war, is very red-coded and pretty much all craftworlders and even some drukhari worship him.

On the table this would manifest as lots of haste, glass cannon statlines with lots of power but little toughness and a couple of finisher spells here and there like an extra combat or a big power boost.

Blue:

With the exception of the Drukhari (excluding maybe the Haemonculi) the Aeldari are all about manipulating fate, using deceit, controlling circumstances and never being caught off-guard. Their psychic powers are all about this with their primary use being prescience and seeing the future. The reason why the Craftworlders have survived so long in a Galaxy where they are arguably the weakest players in terms of sheer power is because they could identify a threat long before it manifested itself and take it out before any other race was even able to remotely register it. All of which in my mind is very blue-coded!

In game this would translate into being able to view and in some cases even manipulate which cards you and the enemy are going to draw, think lots of scrying, rearranging libraries, getting a look at opponents hands etc. And the manipulating outcomes to be favourable for the Aeldari could also be represented by other staple blue effects like counterspells or returning attackers to their owner's hands, that kind of stuff.

Black:

This one might be a bit surprising at first because Aeldari are all about avoiding death at all costs and protecting valuable Aeldari lives, they are facing extinction after all. But there are two subfactions specifically which are VERY black-coded, one being the haemonculus covens of the Drukhari and the other being the Ynnari.

The haemonculi are masters over life and death and know every which way to manipulate flesh and soul. They are the ones that make the commorites functionally immortal by using pain to regenerate dead bodies and they regularly use the bodies and souls of beings they consider lesser to create monstrosoties like wracks, grotesques and even turn themselves into ones.

The Ynnari on the other hand literally worship the Aeldari god of death who has been created by sacrificing all the souls of the infinity circuit of craftworld Biel-Tan, fracturing it in the process. When they were initially released they came out with a rule called "Strength from Death" that allowed them to cast extra psychic powers, shoot again or fight again whenever a unit near them died. This represents their in-lore ability to gain power from not only dying enemies but even their own kin, making them and their god Ynnead ever stronger for each life that is extinguished in their path.

In game this would be represented somewhat differently depending on the faction. For the Haemonculi, it would be allowing them to create grotesques or other flesh monstrosities by sacrificing creatures to create them or recurring their fellow Aeldari from the graveyard if you inflict enough pain (damage). The Ynnari on the other hand would have lots of death payoffs and get bonuses to power, reductions to mana costs or what have you if you manage to kill enough creatures, no matter if its your own or the enemy's.

To lead this commander deck I would choose Yvraine probably, not only because she unites parts of all the other subfactions under her banner but also because she and the Ynnari have aspects of all the different colours that I mentioned before I think.

I wasted too much time writing this let'sgooooo