In my mind Shields would kinda be like a health bar that covers the entire form of the enemy, but some weapon types are good at outright bypassing, penetrating, or just overwhelming shields. Armor would be underneath that would need to be broken down to reveal weakpoints. Not that you need to blast the entire armor layer off the body (which is what ME has you effectively do as its a HP bar), but basically "tunnel" to a soft spot. Effectively creating locational damage points. Certain weapon or enemy types would be effective at punching through armor, or melting it off, or bypassing it through sci-fi shenanigans (psionic mindfuckery, etc).
Then under all that would be the juicy bits that comprise of the most vulnerable systems/fleshy bits that enable the mob/player to survive.
In an Omniframe's case that would be the player pilot, or the power core. If either of those were to fall then the omniframe is basically toast. Core goes down and the player would have to hop out and use a personal defense weapon, player goes down then well, that depends on how the revive mechanics will be approached. If the player is no outright killed then we are looking at a disabled omniframe that is gonna get shredded without the ability to defend itself.
Not every mob would have every kind of defense. Some would be just Health/Shields, Health/Armor, or maybe its not biological at all. A Machine where you just need to either break the power core or render it a non-issue that shuts itself off, but basically just Armor/Shields. Or what if its some wierd kind of energy being thing you need to harvest? Pure shields.