Are you running the MM official build from the website? After I adjusted some settings it has worked snappy. In developer's options, make sure to lower the transition scale and all those to like 0.2. But mess around with the kernel settings. You have HYPER, ElementalX, and SmartassH3 which will give you great performance as for CPU governors, and something like ZEN for I/O will help as well.
I agree with the customization parts. It does lack important features, like navigation bar tweaks, lock screen shortcuts, gestures, etc. I would have switched from it as well, but Xposed will help with that. GravityBox has the answers to most of those. You can swap out a navigation bar for Slimpie, or even tweak the navigation bar. Has lock screen shortcuts as well if you want. I use GB just to get rid of the navigation bar and the lock screen stuff. I use Gesture Navigation module from Xposed for navigating and also some gesture shortcuts.
As compared to the prior PAC builds (I have tried 3 -- Kitkat build had restarting issues, the most updated Lollipop which was a disaster, and an older Lollipop one from marcdw which was pretty good as well, just had volume issues and some bugs), this one is the most stable, and has the coolest kernel. Seriously, this is the best kernel I have tried for Marshmallow, as compared to aCC, Nebula, and 777. I used to use Dirty Unicorns as my main for like 5 months, and while DU had more customizations, I like this PAC-ROM build better because of Privacy Guard and a better kernel. Other than that, they are both rather similar (once you have Gravity Box that is for PAC-ROM). I do miss the Gesture anywhere that DU and PAC-ROM 5.1.1. had though.