It's the opposite -- the Xyphos doesn't really shine in small, "easy" battles like in simulation, but they do much better against fleets, especially when outmatched against larger, higher-firepower fleets like [REDACTED].
You have to consider what ion beams do in the first place. They don't do much DPS -- 50 DPS for 200 flux/sec and 12 OP are pretty terrible DPS/flux and DPS/OP ratios. Rather, the whole point is to disable the enemy's attacks. The more powerful the enemy, the more worthwhile it is to disable the enemy's attacks, because the flux war is a matter of maxing out their flux before they max out yours, and they can max out your flux very quickly. So ion beams prevent the enemy from maxing out your flux, allowing you to max out theirs first.
So the Xyphos is very effective when paired with good anti-shield weapons (hard flux is what gets the EMP arcs to trigger), against high-threat targets. That's the use case for them. If you're in a situation where talons/broadswords can overload the enemy, then it's simply too easy of a fight for Xyphos to be worthwhile. You might as well as just go in with some heavy blasters and get it over with quickly.
Generally speaking your ships will be flux-limited in terms of how much weapons you can equip. Especially in a situation where you're trying to output as much damage as possible quickly, it's usually hard to justify spending 400 flux/sec on a beam which doesn't do much damage. So "outsourcing" that flux to fighters is a good way to increase your overall damage output (in this case, to disable enemy weapons) while still staying within your flux budget.
Additionally, ion beams from fighters (like other fighter weapons) can fire through friendly ships, so you don't have to worry about them being blocked. (This is useful toward the end when you're up against Radiants, and the Xyphos in the rear can still help disable weapons even if the ship is blocked by other ships in the way.) You also don't have to worry about the Xyphos dying because they have a range of 0; they stay by your ship instead of running forward and getting killed.
The PD is a nice bonus. Not only is it omnidirectional (as far as I can tell), but it stays active when you're venting. So you can safely vent without worrying (as much) about incoming missiles. They also form a nice screen (when you have multiple ships together), and remove the need to equip PD.
Furies with Xyphos + sabot pods + cryoblaster (optional, otherwise use heavy blaster) make up the bulk of my [REDACTED]-farming fleet, and the Xyphos is the linchpin to making it work, by disabling their offense so that I can get my attacks in. The sabot pods do a lot of hard flux early in the engagement, the Xyphos disables their weapons so they can't attack me much, then my regular weapons kill them. 7 Furies meaning 14 ion beams on the nearest enemy ships to my fleet. The fleet can handle 2 full [REDACTED] fleets pretty easily, and 3 full [REDACTED] fleets with a bit of luck.
(There's no real reason to fight 3 [REDACTED] fleets at once, since I already get the full +500% XP bonus with 2 fleets, but it's just to stress-test the fleet. The main challenge is this. Usually my fleet fights them to their spawn point at the top of the map fairly early on, and basically ends up making a U-shaped formation around their spawn for the rest of the fight. The ship at the top left tip and the top right tip of the U can take a lot of damage suddenly when a new ship spawns in, especially if that ship is a 5-tachyon or 5-autopulse Radiant, before I'm able to get there in time to save them. The AI, of course, doesn't account for it quickly enough to back off -- it thinks that space is a safe spot, and tends to stay there too long even when given a direct order to back away.)
If you find a better fleet composition that can handle multiple [REDACTED] fleets simultaneously, I'm all ears. If you have trouble with [REDACTED] fleets, I'd recommend loading up on Xyphos on many of your fleet ships. The reason for having them isn't going to be apparent when you're going around chasing down pirate frigates. It's more when you're against heavy odds.
First of all, it doesn't benefit from ITU or DTC. If you're using a ship that relies on range the ion beam is probably going to sit idle most of the time.
If your fleet strategy is to snipe at [REDACTED] fleets, I don't think that'll be very successful. Long-range weapons have low damage output by design and they're not going to take out [REDACTED] ships quickly enough, plus enemy ships are going to close in on you quickly anyway; they're not going to stay back and let you snipe away. Ion beams have a range of 1000 su so that's plenty to be in range along with most of your weapons.
Another reason why it's bad is due to they're not controllable in any degree. Even if set to engage they won't engage the carrier's target. Instead they will just happily shoot anything that is closest to the fighter itself.
They can't move forward to engage because they have a range of 0. They're set to stay by the ship. Firing on the closest target is nothing new, it's basically like autofire. They're there to support.
Last but not least, ion beam is not an instant beam. It takes time to extend the beam to full range which means due to the behavior previously described, it may constantly switch target and resulting in more downtime than it should because the beam takes so much extra time to re-extend on target switch.
That's an odd complaint, because beams are generally more than twice as fast as projectiles, plus they continue to track as they extend (as opposed to projectiles, which go in a straight line once they're fired). While you do lose out on the potential damage as they extend, you do more or less 100% of the damage after that. Have you ever observed how often projectiles miss?
Not to mention, the beam speed is 2400 su/sec, so it reaches this distance in 0.42 seconds, so (assuming the target is at a perfect 1000 su away), this means you lose out on...21 damage. Since beams travel faster than projectiles, this will usually be before the projectiles do their hard flux anyway, and the hard flux is what basically "activates" the ion beam in the first place, so you're not really missing out on much. 21 soft flux which the target pretty much instantly regenerates.
If you're having issues with your Xyphos fighters trying to hop around different targets, then you have other problems. Fighters should be fairly quickly dispatched by your fleet, and if you have multiple ships in range that the Xyphos gets confused over, then it's a positioning error on your part. I haven't had issues with the Xyphos picking wrong targets to go after, since generally speaking
the closest one is likely the one that I want killed in the first place since that's what you want for proper positioning. The exception is *possibly* when I'm trying to finish off a target before it retreats back behind other enemy ships, but in that case, I'm relying on my weapons for damage, not the ion beam which does little damage in the first place.