I am not advocating spam, I am saying use it to maximize damage when you need to use off GCD abilities.
Why would you pop all your defensive cooldowns on the tank immediately, when the first phase of the fight is usually the easiest and your healers have full mana?
You have miasma and thunder between your bio...you are only using 7.5 seconds out of its 18 second duration, how is that "nearly done"? Furthermore, why would you bio before miasma? You can fester during its GCD to again, increase DPS without wasting an animation lock.
Miasma II DOES suck, but IS a slight dps increase if you use it with contagion (about 0.17% dps increase...which is still an increase).
Furthermore, if you're in Miasma II range you are also in melee range, so you can also smack them with your book for another like 0.05% dps increase.
Ruin II lets you use off GCD abilities (like Fester, Swiftcast, Energy Drain and Bane, Aetherflow) without wasting an animation lock. This is another dps increase. Furthermore, during that, you can autoattack for more damage.
I was taking you seriously until you said to not use Shadowflare. Even if it did no damage, shadowflare provides a chance to slow the boss, lowering his damage on the tank (much like Eye for an Eye, except constant ticking chance to proc), and making it easier to interrupt abilities. Add in the fact that it DOES do abilities, and that it lasts 30 full seconds, and only costs slightly more than Bio II, and you have an ability you should always use unless the boss is going to move.
Furthermore Shadowflare is by far our most efficient DoT if used on more than 1 target.
Miasma II is also a dps increase on more than 1 target, though dot + bane is better, and with 4 or fewer targets tab targetting Thunder is also superior.