Players will almost always make the most efficient combat decisions they can. The advantage to focus fire is that it more quickly reduces incoming damage by reducing the number of combatants left on the battlefield in following Phases/Turns. In order to discourage Tactic #1, you have to engineer situations where it is no longer viable. So in order to render the tactic ineffective or impossible: you have to create a situation where Focus Fire instead increases the incoming damage, negates its ability to reduce the number of combatants on the battlefield, or makes the opportunity cost higher in some other way.
Of course, if it is fair for PCs to do it, than it is fair for NPCs too. If PCs leave themselves open to Focus Fire, use the tactic against them.
What if there were a group of metahumans (like a small tribe or family unit) who all have small amounts of Usable By Other defenses which they can apply to others instantly via Triggers. In this situation Focus Fire becomes ineffective because the NPCs can similarly Focus all their Defences on whichever of them is being targeted. The values should be such that if all of the NPCs Focus Def on one of themselves, they are effectively immune to the PC's attacks. However, if the PCs spread out an attack each member individually, their own defenses (sans Focus Def) aren't enough to protect them.
What if you simply develop a single NPC specialized in combat against multiple opponents. All of their defensive characteristics increase proportionally to the number of Attackers they face. Such as a character with Regeneration and Absorption As Defense to DCV and/or DMCV (as appropriate). Likewise, a character with bonuses to various CVs dependent upon facing multiple Attackers would also be effective at discouraging Focus Fire
What if the Villains/Agents the characters ignored are able to escape (and target their DNPCs next). Or worse, what if they take and threaten hostages immediately; thereby forcing characters with certain levels of Code Vs. Killing to make Ego Rolls to resist the compulsion to engage the hostage taker instead.
What if the first combatant on the scene is a Brick so tough the party can't hurt him, but can't really hurt them either beyond harrying (for whatever reason), and only after the heroes begin to Focus Fire on the Brick do the come out of the Woodwork to finish the PCs off, or accomplish their objective. For example, Brainchild could persuade Ogre to start a street brawl with the heroes to buy him time to perform some villainous act or another.
Regarding Optional Rules: I can think of two optional rules which discourage Tactic #1 as consequences of their function. The first is Wounding (CC 160), and the second are the Damage To Subject and Injury (HSS 34 & 35) rules (which are the same as the Significant Injury rules from Fantasy Hero 5th Edition). Both optional rules in some way undermine the core principle that allows Tactic #1 to be so effective: The fact that it doesn't matter how much damage the defender has taken unless it results in their immediate incapacitation. Aside from the chance of being Stunned, there is no penalty assigned for having taken damage. In other words, by default, the first strike doesn't matter, only the last (which isn't very realistic).
The first, Wounding introduces a chance that taking damage will prevent the attacker from performing offensive actions (in addition to the chance of being Stunned); which means the more the attacker's spread out their attacks, the more defenders they can potentially Wound or Stun that phase (thereby reducing incoming damage without having to be able to reduce the number of remaining defenders).
The second, Injury, introduces a "death spiral" effect wherein the defenders are less able to retaliate as they become more and more wounded. Which again, means that spreading out the attacks allows them to potentially Injure more defenders (thereby reducing incoming damage without having to be able to reduce the number of remaining defenders).
Other Notes: In order to further ensure that Tactic #1 is discouraged, you mustn't let the PCs know when Tactic #1 is working. Don't report exactly how much damage is being taken beyond what is obviously visible. Otherwise once they realize a target isn't taking enough damage to drop them, the player will switch to a "softer" looking target even if there is no good reason for their character to want to do so.
I don't really consider the amount of damage taken by a attack to be obvious to the attacker unless it causes actual destruction (such as breaking an enemy's bones or putting a hole in a wall), so I describe my enemies status in vague terms so that the players cannot make decisions based on information their characters should not have.