[Nexus 6P General] Spartan117H3:
My opinion from the other side of the spectrum (feel free to correct me if any information is wrong/if you believe I'm mistaken):

I feel like people are running the wrong rom, don't really use their phones for anything except for very basic, simple tasks (which is fine, everyone uses their phone for different things), or they don't know about a lot of cool things that they can do. However, the Nexus is well known to be a Developer phone that allows you to unlock and modify it as you please. It was a major selling point for me, especially since I came from a Verizon S5 with a locked bootloader and only root access. It also has a huge developer community here because of the freedom it gives.

TL;DR: I have two parts, part 1 explains why the OP is misguided, part 2 is a list of what I use personally.

Part 1

: TL;DR, OP most likely messed something up, or installed something experimental/buggy. His claim from his experience is that stock is better. In reality, stock prevents him or whatever he installed from messing with things he shouldn't be messing with.

Not trying to instigate anything, but I believe the OP is completely misleading in his claims.

1. Claim: 100% stock with a custom recovery and systemless root runs fine, then starts slowing down.

Response: Custom recovery only runs when you boot into it. It is separate from the ROM environment, otherwise you wouldn't have to reboot/exit the rom. Root (SuperSu) just asks if you want to give an app higher privileges. It logs when an app is granted/accesses these permissions, but that doesn't take much. Lag from these two doesn't make logical sense.

2. Claim: Random lags, freezes, drain.

Response: Not random just because you don't know why it happens/didn't seem to troubleshoot it.

3. Claim: Google intended for us to

only

be on 100% stock

Response: Why don't they lock the bootloader like (i.e Verizon & AT&T), install a hardware fuse that trips if the phone is rooted, and deny warranty claims for messing with it?

4. Claim: Stock experience is the "best"

Response: If so, why does Android slowly implement things that were only once available exclusively to root/custom roms (Doze is similar to a weaker global Greenify, System UI Tuner is a minimal rip from basically any rom's customization settings, 6.0's limiting permissions for apps is like a weaker xPrivacy, phone number blocking was on rooted phones first, Google's apk restore from the Play store is very basic whereas Titanium has been out for many years )? Two main reasons, stability and the end user. New features allows more possible bugs/errors/etc. End user - the majority is the target audience (most revenue), so the goal of the developers is to 'dumb down' the software enough that 'anyone' can learn it, put in some advanced features that will be used by more knowledgeable people, lock it down so users at either end can't break anything, and last but not least, prevent people from exploiting flaws in new features. Note: The target audience does NOT include Root users, which are the minority. Root means greater permission level meaning it's easier to break everything. If you think about it, root/rom users get "experimental" creations to test and make better.

Statements from OP:

5. I miss adblock.

Response: Did you know that Adaway actually slows down the loading of web pages (more noticeable if there are many filters/exclusions/wildcards)?

6. Earlier OTA updates

Response: Monthly security patches are great, but they're more for high level exploits, not so much patching bugs. Do you know about the Android 5.0 memory leak? Google knew about it for a long time but didn't do anything. An Xposed module was released fixing the issue. A LONG while later, Google released 5.2 to fix the leak (5.1 and 5.1.1 did not). However, not all carriers pushed it out/some didn't at all. Then there was the stagefright exploit which received a lot of publicity. Google decided to try and set the bar for Android updates and encouraged others to follow suit to fix problems faster.

7. Claim: You think Xposed is slowing down Marshmallow and is giving it issues

Response: No support, no evidence, no list of modules used, no claims of attempting to fix it, log submissions, or troubleshooting steps. Just a hunch, kind of like your hunch that stock is better? I used to have a lot of modules on my S5 but have very few on my N6P (the custom rom covers a lot of the things I need/want).

The only times I experienced lag (keep in mind, these cases are very rare):

1. Playing a 3D graphics heavy game for a few hours (the phone is noticeably warm). The reason for lag is obvious, it's not of any fault to the phone/rom, but rather what I am doing.

2. I recently restored ~60,000 text messages (because I had to RMA my phone and I like keeping texts), and the application 'closed' a few times. But I know it is partly because of the app (doesn't like being run for long periods of time but it will allow you to resume if you reopen it), and because of how long it ran for with the screen on while plugged in (~8 hours). Reason for lag is obvious, same as 1.

3. When an application is inefficiently coded and lags/closes. Not a rom issue unless the rom is taking up all the ram and/or processing power, at which point, System apps should also force close and/or lag.

Part 2

: TL;DR, I am not the average user. I use many things that people (mostly those who are on stock) probably haven't heard of, or may not have a use for it. Below is a list of some of the apps that I use.

I consider myself an OCD power user. I spend hours trying to tailor my phone to my liking. If I can think of a feature I want but isn't available, I'd request for it or find a way to get it done.

For the record, I have only used one rom on the Nexus 6P, the PureNexus Rom - It has many of the things that I want, has a great/active dev that implemented some of my requests in the next release of his rom.

I probably have enough examples here to cover for everyone who says they don't use anything and run stock:

1. App Clutter/bloat: Anything I don't use or never intend to use is bloatware to me and should be forcefully removed, assuming it doesn't break anything I need. ( I.e Google Plus, AOSP Dialer/Contacts/SMS, Drive, etc.)

2. Visual Clutter: I use NotifyClean (Xposed) to get rid of anything I don't want to see (especially notifications that must persist in the taskbar, WiFi networks available, specific notifications without disabling it for an app entirely, etc. Nova (root isn't required for this) launcher to hide apps I use rarely, or those that have a background task and doesn't need to be opened often (I.e LightFlow, Miband Tools). Hiding status bar icons/network traffic, I keep bluetooth on all the time cause of my MiBand, so I don't need to see that it's on. I also use Adaway for adblocking.

3. Visual Eyecandy: Layers. I use Domination layers which makes many things black which makes things much easier on the eyes. Layers allows a much higher threshold of modification for looks than stock does. I also sync contact photos from Facebook to my contacts on my phone (requires root, and is the only way I've ever found that works ever since Facebook stopped supporting it).

4. Battery Life: Kernels with profiles, and Doze settings editor. I don't see much benefit with this except it drains less battery when not in use. But I use my phone a lot/charge it a lot (I don't like a low battery), and am too lazy to log my usage to compare results. Google created Doze in android 6 whereas root users were using Greenify for a long time before that; greenify is more powerful than Doze if you're into that stuff (I don't use greenify)

5. Functionality/ease of use: Custom quick settings where I can define the number of columns per row, smaller navbar icons, hold back to kill a rogue app (due to an app issue, not because of the rom itself), holding recents to get to last opened app, clearing recents, disabling power menu/quick settings from lockscreen, forced expanded notifications, weather in various locations, disabling vibrate on unlock, custom steps on volume, sliding over statusbar to control brightness, power button hold for torch, double tap for camera.

6. Power User Apps: TWRP Recovery - You could survive anything short of a hard brick/bricking your phone with a locked bootloader (from the OS). Titanium backup - backup and restore all the data that you want to migrate to another rom or to use in a clean install. Cerberus Anti Theft - allows you to track a lost/stolen phone, take photos, wipe phone, etc. An app that I have been trying to teach myself Tasker which allows you to automate many things on the phone. I.e. open/play music app when paired with car bluetooth, Google Now with GPS/traffic lookup before going to work, you can also make tasks to do things that Cerberus Anti Theft does and more. If you lose your phone when it's on silent, you can make Tasker put your ringtone to max volume and ring and/or send you GPS coordinates.