Mass-effect – weak point on an Atlas

Like in Mass Effect 2, each individual weapon has different base damage values against Health (Red), Armor (Yellow), Shields (Blue), and Barriers (Purple).

The information linked to in the post is true for the general case - most Pistols deal the most damage to Armor. But you have variance between the individual weapons as well - the Arc Pistol is a pistol that specializes in dealing maximal damage to shields, not armor.

The exact benefit against any given defense depends on the individual weapon. (Melee and the various heavy melee abilities can be considered as weapons in this case)

That clarified, Armor, Shields and Barriers provide absolute protection until they fail (they are effectively a separate health bar), barring special abilities suck as the armor-piercing weapon mods (which allow some damage to 'penetrate' armor), and armor piercing ammo (same).

Power recharge doesn't affect Nova since whether or not you can use Nova depends entirely on if you have shields or not. The biggest point of the power recharge is to make your Biotic charge have a lower cooldown so you can go into a crazy Charge->Nova->Charge->Repeat cycle until whatever you are targeting dies.

If you are comparing absolute DPS, the Charge->Nova->Charge->Repeat combo can't be beat. The reason behind this is that, once your power recharge rate goes up high enough, your charge will be instantly available right after a Nova, and rather than doing a second nova at half damage, you can do a full blown charge at max damage. Since this is the case, you want your only nova to do as much damage as possible rather than just 60%.

However, if you worry about survivability, then you can go for the half powered nova so you retain some shields.

In my first playthrough, I went the entire game using the Charge->Nova->Charge pattern (difficulty hardcore), and I had no issues with survivability. Just don't do something silly like Charge into a banshee and get impaled.