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Strikecraft will fall behind horribly ~around level 20-30 in energy weapon :)
a) weigh up the pros and cons in situations to see who counters who, or if its balanced
b) just play it for flavour as long as they haven't shot themselves in the foot (see a).
The only reason I can think to use torpedos, and only on a missile corvette, is to hard counter enemy battleships that are not using hangar units.
The only major reason I can think to use swarm missiles is if you and the enemy both use hangar units, or the enemy has a lot of PD that is killing your hangar units.
Note: you should only be using missiles on corvettes. Hangar units with the carrier computer are superior to missiles in every way.
When you fire an energy weapon there's no lag between hitting the enemy and reloading because they're instant hitting the target, adding torpedoes isn't supported by the game because:
a= there's no range modifier who makes missiles launch them where it won't take a week for it to reach the target
b= they're too weak in dps vs battleships energy weapons
c= there's no retreat mechanic who works with missiles since they'll just vanish once you jump
d= they're destructable
e= them ignore shields making them useless in support of other weapon types
f= their weapon slots are on ships who can't have only missiles onboard
Only in a truly dichotomic situation would most of the answers presented of what's optimal, would actually answer that swarmed missiles and torpedo are not viable because they are not optimal.
e) Assuming your missiles aren't getting shot down by enemy point defense, they pair just fine with anti-shield weapons. The reason is that the anti-shield weapons will do well against the shields and then stall out against the armor. Pairing those weapons with missiles means that while the anti-shield weapons have been working on the shields your missiles have been working on the armor, which means that your anti-shield weapons will have less work to do at their anti-armor penalty rate, which in turn means less time spent getting to the enemy hull.
f) This would be an issue if missiles could not be paired effectively with non-missile weapons, but as I just explained that is not the case. So, you fill your missile slots with missiles and then fill the non-missile slots with anti-shield weapons and you'll be good (depending on the availability of enemies without point defense).
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However, there is another reason that using missiles is disfavored:
g= Because missiles and anti-shield weapons and strike craft are all in the engineering track, they compete with each other for repeatable boost techs. If you combine any one of those three with anti-armor weapons, which are in the physics track, then you can get your full research rate applied to all the weapons you use. If you use more than one of the engineering track weapons on your ships, then you split your research rate among them, which makes them all weaker than they could be. So the better choice is to use anti-armor weapons and one of the engineering track weapons, and the best pairing with anti-armor weapons is anti-shield weapons because it will decrease your time-to-hull the most.
Instead of anti-armor weapons from the physics track you could use the bypass weapons (disruptors), which is fine. They should not be paired with any of the engineering track weapons, though, since those will all have to wear through shields and/or armor, which will dilute the advantage of using bypass weapons. If you did decide to mix weapon types then you would want to pick just one engineering weapon type so that your research on repeatable techs is not diluted. Either missiles or strike craft would be the better choice here, because at least they bypass shields. Unless your enemy is not using point defense (and they probably do have pd), you are probably better off using only the bypass weapons.
So my conclusion is that the best choice against the enemies you are likely to encounter in Stellaris is either pairing anti-armor and anti-shield weapons on your ships, or possibly using only bypass weapons. Strike craft could potentially have a role in your fleet as a defense against enemy strike craft. Missiles, though, are just strictly disfavored since there isn't a ship design that makes good advantage of them and also keeps your repeatable tech research focused.
But is not an absolute.
Regarding repeatable bonuses, arguable strike craft IS the best due to better scaling AND the fact that Shields and Armour have repeatable percentage scaling while Hull has only a single flat (admitedly good proportion) increase. So while you said:
I would give the premise that its because back line battle ships escorted via fighters is far better than wasting smaller class craft guarding ones that get past your front-line engage fleets, as well as these fighters can still scale harder bypassing those heavy scaled defences straight to hull.
conclusion
Sure go missiles for your anti armour, but it has both pro's and con's.
If you get a portal Physics-NVB or spotting Tiyanki Space Whales to go Society-ES; either can fill your anti shields weapon.
Though you can skip this or switch over later to Physics penetration/bypass (NVB, CL, AE is a nice route).
Best scaling repeatables is Physics Energy weapons, Engineering Strike Craft.
1) Strikecraft are still forced to deal with armor.
2) Strikecraft waste time flying.
3) Strikecraft have fixed HP so in theory - on very high level of repeatables it will be wiped by PD regardless of their buffed regen.
4) As I'd already said - around level 20-30 in repeatables Arc Emitters became too powerful (when you're using all available buffs) and simply burn through AE fleets before strikecraft able to reach them and deal any notable damage.
I think it's obvious that ordinary empires are even less durable against Arc :)
Even small ships are not able to survive - sure, they will dodge 20-30% of hits... but this hardly matter as usually a single hit from Arc on such levels of repeatables is enough for corvette.
I tried so much to pull fighters into endgame... But usually even single CL on my BB deal more damage :(
Let's do a bit of math. How high our chances to hit a 90% evasion corvette?
Our tracking is : 0% + 15% (sensor) + 10% (titan aura) = 25%
Resulting chance to hit is 35% (up to 45% if you're crazy enough to use psionic, +10% more if you're using enigmatic decoder - and it's still a viable decision).
Don't forget that AI using quite few corvettes in endgame instead of massing them.
So ...I don't see any notable effect from using strikecraft after all this calculation. Sure, they would be nice to have against Pretoryn... But I would prefer more CL against Contingency. And Contingency is what's really matter among all possible crisises.
I believe only a few modifiers actually work on strike craft. Only PDX dev have the full picture.
Even modders struggle to get anything working last I checked on mods for strike craft.