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There is a paid version that eliminates the adds, but its actually pretty decent. My wife hated the fact that I couldn't get Gif's what I would recommend is Textra Textra lets you send Gifs, customize the look and feel of your messaging app and do other fun things. The one thing I guess your probably going to miss is a Gif keyboard. Simple things like this help me in my day to day operating with my phone.
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With nova I've set custom gestures, like double tapping to bring up my app drawer, and swiping down to toggle my notification tray swiping up with two fingers to access settings. So in essence Googles Marshmallow Os> Samsung Touchwiz>Launchers (Nova Prime in my case).
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Launchers are like skins that go on top of your OS. That comes down to what you like and how you feel. Then you have Samsung putting their own flavor on top of that calling it touchwiz or Htc with sense. So for instance your running version 6.0.1 of marshmallow that's Google's operating system or OS for short. What happens however is that each company puts their own spin on top of android. Similarly to how Apple simply has IOS across all devices google wants to run each iteration of its operating systems across all device companies (HTC, Samsung, Lg). Stock is, for all intents and purposes, what Google wants to have all their platforms run. Some people love the simplicity of Touchwiz, others hate it. Personally I hate it, but I've figured out what and how I want MY device to look and feel. The issue that you run into, is that with more die hard android users Touchwiz can seem too gimmicky. Standard launcher ( Touchwiz) is a fine daily driver (what you use on a regular basis). To answer your questions in order and from a personal standpoint:
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