There is no way missiles are a threat in PvE unless people want it to be. In general it's a better idea to use shield instead of hull tanking in PvE, thus missiles are irrelevant in PvE unless one intentionally makes oneself vulnerable to it. PD's ability to shoot down limpets is only relevant to cargo hauling, its ability to intersect missiles is completely overshadowed by other utility such as chaff/scb/sb, especially in PvE.
WRT missiles being irrelevant in PvE - you must be playing a different game.
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PD beats chaff under at least some circumstances because it is automatic and has much greater ammo capacity. That does not mean Chaff is pointless though, far from it does have it's place but it is far from a 100% countermeasure to incoming fire.
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As for the SB v. PD question, the situation is more complex and they address different concerns. An SB is of little use against missiles when the shields are down.
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As for SCBs, again they do not help when the shields are down and are far from automatic BUT again they may have utility but IMO there are better things to spend a slot on unless you have slots to spare.
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ECM v PD is more complex, but essentially ECM still does not overshadow PD and ECM probably complements PD since it is manually triggered and does not require ammo.
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PD proves it's worth when you are running and have lost your shields for one reason or another. It's power usage is also low enough that with power management it can still operate on most ships even after the Power Supply has been knocked out.
The problem is that SR already has heat consequences, so nerfing it flatly instead of introducing some counter mechanic is decreasing variety. Not to mention that SR has limited and predictable operation time based on the ship's weaponry and HSL amount.
Nerfing it is probably needed to counter the "missiles are pointless" argument, and who said anything about nerfing it flatly? As for counter mechanics, that is addressing the symptom and not the problem which would seem to be an over dependence on the stealth mechanic in combat under at least some circumstances. Whether it needs dealing with on a ship by ship basis I don't know, but if people are depending heavily on stealth in combat it does not lead to a healthy balanced game overall - it would not matter as much in a PvE only game but in a PvP-enabled game it just does not ring right
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Courier is one of the lightest ships, no matter how much weight it tries to put on, it doesn't compete with true large crafts. Also, ramming is a valid tactic, there is nothing wrong with it. Ships that can't maneuver out of its way don't have to worry about ramming damage as long as it's not light-weight build, ships that can maneuver don't have to worry about it to begin with. Courier isn't that maneuverable.
I know people who would disagree with the Courier being not that manoeuvrable, one of them being a friend of mine who considers it one of their favourite combat ships... and AFAIK they did not make use of SCBs.
The balancing of SCB was done out of the complaint of lack of variety and specialization of PvP and PvE ships, ships like Courier and Python just get caught up with these changes and become less and less competitive. Courier had a place before, not anymore.
If you rely on the pre-v1.5 SCBs to keep competitive then perhaps the problem is with player expectations as opposed to the ships themselves.
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Overall though, I thought the pre-SCB nerf situation sounded a lot like an exploit rather than an intended mechanic. WRT Stealth, I do not believe FD intended ships to use the mechanic as the fundamental basis of a build, thus could be considered an exploit from a certain point of view... How to address that situation though would by necessity need to be done carefully (possibly requiring public Beta testing to ensure the balance is right regardless of the PvE/PvP status). Stealth should be effective against NPCs but should not allow ANY ship to lay in wait and ambush other players near stations (c/f Stealth camping/loitering). If the NPC ignoring of Stealth was an intended change, then that is the main reason I can see for FD doing the change - to address Stealth camping.