I didn't notice this thread till someone pointed it out to me (tip: if you really want me to see something, send me email through the site). I will take a look and see if there's a bug throwing off the numbers for herbalism. I will note that herbalism is not averaged on the site since it's a haste cooldown- it's treated like a haste proc and is included in the simulation at expected intervals. It's possible there's a bug so I'll investigate over the weekend, but it's more likely it's just causing shot shifts that are having a larger effect than you'd expect. You could turn on the debug output and compare with and without the CD side by side and see if you can tell why the numbers are changing by so much. I've also heard for some caster classes herbalism is actually one of the best professions now because of RPPM, but I wouldn't think that'd be the case for us so it's definitely worth looking into.
Since the engineering gloves are an agil bonus, they are averaged over the course of the fight so you will not get an accurate picture of their value, since normally you would stack them with CDs.
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The reason the cap is 20 seconds is because some of the abilities it delays for have a 30 second cooldown, so it'd basically delay indefinitely if it didn't have a cap. With the changes coming to readiness I will most likely change this. But if you are looking to simulate with a higher degree of accuracy and control, simulationcraft is a far better option- there are limits to what I can support via a web hosted service.
I found the issue with Lifeblood and fixed it. It was actually being simmed correctly in the rotation, but for some trinkets the uptime needs to be calculated before the simulation has been run, so uptime of Lifeblood is estimated to be included in the RPPM proc rates, and there was a bug with the estimation part of Lifeblood uptime which was leading to RPPM uptimes that were too high. Now that I've fixed it, it shows as a small decrease from alchemy for me.
Engineering and one other is the way to go. Rocket boots can be valuable in certain scenarios or you can have the bomb tinkered to your belt for more deeps. Enchanting is a solid gold maker.
Useful on Lei Shen Helm of command even if you have disengage glyphed, or AoTC glyphed, rockets boots have saved my ass many a time when I've not had a resto druid Symbiosis me and give me dash, although they have killed me once or twice, but more often than not been a life saver.