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Shackles were bad for combat because if I bring two friends and have five minutes to work something out there is noone in imperian past or present who isn't going to die. Its a licence for a free kill and that is dumb. There is no degree of quick reactions or smart play that is going to save a person in that situation. Personally I used to just doomworm because why bother.
Chains are actually (slightly) more balanced because 1 minute is somewhat more reasonable - this means if the people attacking you are incompetent you do have a shot at surviving. The problem is chains last too long - I have enough chain charges that I probably would not have ran out within 5 years of active play and I did not buy heavily into chain rewarding promotions. Shackles are a (very debatable) limited resource. Chains are a staple that superceeds every other hinder skill in the game.
Personally I'm opposed to mechanics like this in general though - I'm of the mind that you should have to exert some degree of effort to force someone into a fight that they have no mechanical recourse of evading. Its why I went out of my way to make greensharding me as miserable an experience as possible.
Making shackles/chains block exclusively special forms of travel is a superb solution, imo. It preserves the use against powerful artefact escapes (and skill escapes too, but that's probably fine) while meaning people will still be able to escape the situation if they play well.
Generally it only takes one person to highlight issues. I'm not going to get into the argument about whether there are in fact issues, but that's actually usually how this tends to work: somethings considered fine until one person comes along and proves otherwise.
It usually means you're doing something right.
Chasing out of the shardfall seems like common sense to me. If someone ducks out mid fight/right after harvesting chasing seems like a no brainer. If you're chasing them half way across the map you're probably being excessive. Call me a jerk (you'd be right) but if someone is afk in a shardfall area they can take it as a lesson for why afking in public areas is bad for their health.
I personally don't think you should be able to retaliate from someone defending their city - this is an instance you are instigating conflict and the city defenders are protecting their interests. The onus should be on the aggressor to suck it up and take their lumps, speaking as a former prolific city troller. City defence is a great way to draw people into pk, that ceases to be the case if some competent pker is just going to curbstomp you when you go to bash later because they didn't like how things turned out. To draw a comparrison, this is like me going and jumping someone then because they hit back I go jump them again when they get back to life. It is possible I'm misunderstanding the stance on this, but those are my thoughts on it.