These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternative Character Interpretation: Is Mare Do Well so self-absorbed that she simply doesn't care about how much she's hurting Rainbow Dash by screwing with her perception of her friends, just so long as she has Dash's attention? Or does she not realize the full degree to which she's damaging her? Or is the game spinning out of control, like in Chapter 9?
Broken Base: Long before Mare Do Well was ever unmasked, readers became split over whether she even deserved a shot at a happy ending, or if the way she lied, deceived and manipulated her meant Dash should chew her out and dump her once she learned her identity.
Unsurprisingly, after The Reveal and the inevitable Ship Sinking that followed, some of the readers who were hoping for MDW to be someone else were less than ecstatic.
The Ship Sinking isn't all that inevitable, though, as Dash seems to resolve to try to work things out anyway. Leading to another group of readers (such as this troper) that aren't too happy about the reveal but still hope things turn out well.
I Knew It: A handful of readers thought Mare Do Well was Pinkie Pie. Another handful hoped otherwise. One group was vindicated in Chapter 20. Take a guess which one.
True Art Is Angsty: AbsoluteAnonymous states in her "resignation letter" (since deleted, along with her entire FIMFiction blog, but an archive can be found here) that she began writing MLP fanfiction as a way of coping with emotional issues she was going through at the time. While it is not explicitly stated that The Games We Play was the direct result, it would take a stretch to infer otherwise.
The Woobie: Rainbow Dash, Pinkie Pie, and Mare Do Well are all this at some point. Pinkie especially. To clarify:
Rainbow Dash suffers multiple injuries and is grounded a lot of the time, so she cannot turn to flight to help mentally sort things out as she usually does. She is beginning to get over her head, has a hard time sleeping, and only gets any rest at all while hiding in a bush. Furthermore, she is becoming increasingly torn between feelings she might have for Pinkie and those she is developing for the Mare Do Well.
Pinkie Pie feels she now has to compete for something she never thought she had to defend. She ends up confessing her feelings to Rainbow Dash, only to be shot down. Dash continually brings up the Mare Do Well when she is around and will not confide in her. She is desperately trying to win Dash's affections, but is resigned to just maintain their friendship for now. She also becomes a Stepford Smiler because she thinks her friends will stop liking her if she's not happy, but is really hurting underneath the facade.
The Mare Do Well is clearly in way over her head. She is pretty much making everything up as she goes, and is pretty much reduced to asking Rainbow Dash whether what she is doing works or not. She really wants to drop the pretense and disguise, but feels that Dash will hate her for the deception. She also unintentionally gets Dash injured while trying to win her affections.
Jerkass Woobie for Mare Do Well seems more appropriate, due to how she seems obsessed with continuing the game to get the most out of it for herself, seemingly unconcerned over what it is doing to Rainbow Dash and her relationship with her friends.
Pinkie Pie again, after The Reveal. She essentially was a Stepford Smiler all along and only invented the Mare-Do-Well in order to escape having to act happy when she really wasn't. She also reveals that she truly has multiple distinct personalities, and she knows full well just how crazy she is. Furthermore, she's absolutely convinced that she cannot help herself and that she's broken beyond repair.