As someone mentioned, you can create a custom APL (action priority list) for your class/spec. Basically, you set the conditions for when you will use spells and under what conditions. May take a while to get used to the syntax, unless you're just making minor adjustments. I still use custom APL's for some classes/specs because default ones haven't always been the best and tend to sim lower, whether by accident, bug, or intent. Heck, I use custom boss scenarios that are tailored to actual boss fights versus just Patchwerk/HAC, especially when taking damage can affect your DPS output/logic. You can easily adjust the sims according to your playstyle if you know how to program it (there is documentation linked on the raidbots site, I believe).
People need to keep in mind the sims are a tool that's only as smart as you program it to be, and I'd say the majority of people probably aren't using them correctly when trying to figure out what's best in various scenarios. I had a recent scenario where my guild was having people sim a certain BoE w/ corruption to see who would gain the most benefit out of it, and everyone dicked up their sims in some manner to where the information they provided was vastly wrong. If you just want a "close enough" answer, that's closer to what most people are likely getting. However, I still get people asking me how their gear is simming one thing and are confused as to why they're doing everything right and the logs don't reflect the sims. Generally a case of people not using a tool correctly, then blaming the tool for being bad.