not going to argue that violent runes as a whole are a bit too strong. They are. However, I don't find your proposed changes or suggestion to remove them feasible.

1) Rune packages. People have bought rune packs. I'm betting a good majority of them buy violent. They bought them with the awareness of how strong violent runes are and how difficult/expensive they are to obtain. Sure we can argue that they have the same chance to drop in dragons as shield runes, will runes, etc. Its still doesn't make it less rare/difficult considering how rare 6 star runes in general are, how hard it is to get a % rune of the desired set or even good substats on a 5 star 1/3/5 rune. These low chances of obtaining a great/usable rune apply to all rune sets, but they aren't as overpowered and valued as violent in many cases, are less expensive in the shop in comparison to violent, etc.

Now, if we change how violent runes work or remove them, customers who bought said rune packages for violent runes either no longer have the runes they bought, or the product they bought no longer works as advertised. You can argue that its all rng and someone who buys a wind pack in hopes of getting a certain monster should deal with it in case said monster gets nerfed and "no longer works as advertised." In this situation however, even if the rune package gives a person crappy violent 5/6 star runes, they still bought it because the package guaranteeds no rng in terms of getting 5 or 6 star violent runes (at least 1 6 star) in the first place because a 4 set of crappy violent runes used together still gives the set bonus. If I remember correctly, rune packages arent guaranteed to give a full 1-6 slot set, but if for example they get 3 slot 1 violent runes and 3 slot 5 violent runes, they at least have the option to farm faimon hell in the various stages to make a full set.

If either they are removed or nerfed, People will demand refunds (and most likely get them, while also keeping the benefits of long-used crystals they received), or simply stop buying rune packages. Com2us is very concerned with profits mind you in this f2p game that survives off people buying packages.

2) your proposed change makes sense mathematically in terms of providing a bonus that is competitive to swift. Every third turn, they get an extra turn, so their fourth turn is free (and as you mentioned the counter is set to 0, so I assume you mean they dont get a buff on the fourth turn). I'm not going to work out the math, but overall you are missing the big picture. Swift would in most cases be preferred even if your proposed changes work out to a turn advantage with violent over time with the changes. Swift runes will at least let the monster move faster, and receive three turns faster over a monster on the new violent set in the case they have the same base speed, spd substats, etc. Even though the bonus of swift has diminishing runes as you stack speed, id still take it in most cases over your new violent change. Now add atb buffers/spd leader bonuses/etc. three slower turns and an extra turn doesnt outweight 3 faster turns and possibly a 4th.