For purely physical damage (Tanking towers on accident is a thing that Yuumis do from time to time :P), 2 armor is the best option. For purely magical damage (sometimes you need to proc your passive, or attack the minion wave, or hit a tower, and you might get hit by something magical), 2 MR runes is the best option, but if you're dealing with mostly physical and some magical, or vice versa, taking the correct resistance + health is less effective against the main damage type, but more effective than double resists against the opposite damage type.
If you expect even amounts of both physical and magical damage, then the best option is to take MR AND Armor. The health rune is NEVER the most effective unless you take it with one of the resistance stats, which I typically do (usually armor) along with Adaptive force on the first rune. Taking double adaptive force + health is ALWAYS the worst choice compared to double adaptive force + armor or magic resist.
At level 1, Yuumi has a base armor of 25.
Using the formula: "Effective Health = (1+(Armor/100)) x Maximum Health" we can see that 25 armor gives Yuumi 25% of her maximum HP as bonus effective health, so her actual HP value at level 1 against pure physical damage is 600.
Add 6 armor to that, and we get "Effective Health = (1+(31/100)) x 480 = 628.8 HP at level 1 against pure physical damage
If you take 2 armor runes, you get (1+(37/100)) x 480 = 657.6 HP at level 1 against pure physical damage.
If you take 1 armor rune and 1 HP rune, you get (1+(31/100)) x 495 = 648.45 HP at level 1 against pure physical damage.
Yes this is lower than taking 2 armor runes, but as she levels up, this amount scales as well, and 2 armor runes does nothing against magical damage at all, where 1 armor rune and 1 hp rune at least gives you 15-90 HP per level against magical damage, as well as scaling multiplicatively with the armor rune, making the armor provide even more benefit as the game progresses.
The same thing goes for the MR runes / HP combinations, same formula and everything.
If anything the armor rune is slightly underpowered at 6 armor vs the 8 of the magic resist rune, since physical damage is so much more common in the game (minions, towers, and monsters aside from baron and gromp deal physical damage, as well as most champion basic attacks.)