The author notes on multiple occasions that her opinions are unpopular, as if it were some sort of badge of hipster honor. It seems to me that any unpopularity would stem from the generalizations and misconceptions rather than the opinions presented being incredibly revolutionary -- of course there is bad writing in indie games; there is bad writing in every medium. The idea she presents that using unoriginal concepts naturally leads to lower quality doesn't fly, either.
Yes, innovation can lead to a wonderful game (see: Bastion), but it can also lead to shit (see: Gears of War, and the ensuing series of chest high wall simulators [no hate against the game itself, just that 'innovative' mechanic; Gears may not have started it, but it certainly popularized it]), just as repetition of past ideas can create great games (see: CounterStrike: Source; Terraria, KAG, etc.) just as easily as it can create shit (see: Every Call of Duty past World at War). Just because a good idea has been done before doesn't mean a new developer can't do something great with it -- the idea was successful because people enjoyed it. Just because an idea hasn't been tried before doesn't mean it is good -- there is quite possibly a reason why it hasn't been tried before.
Halo 2 and 3 were hardly innovative, with little more than some graphics upgrades and mechanic changes/additions, yet they were some of the most successful and popular games of their generations; Halo 2 was pretty much singlehandedly responsible for popularizing console online multiplayer. Quake III: Arena was hardly much different than earlier FPSes of the original style, yet it is still played today.
Even the emphasis on good writing is a flawed idea at the heart of it; the best games are not those in which the railroad tracks are gilded. The vast majority of games which I adore either are completely open-ended (see: Aurora, Cataclysm, DF, any RTS, TBS, or 4X) have fairly open-ended gameplay in which the main plot exists as little more than a trail you can follow for a bit of extra loot and experience (see: Elona, Morrowind, Fallout: NV, etc.) or have little/no story at all, focusing on quality gameplay mechanics and exciting moments (CounterStrike:S, Day of Defeat:S, Frozen Synapse, Alien Swarm, KAG, any of the many Touhou games, Just Cause 2, Ace Combat 6 (Gog yes, that mission where you fly down the barrel of the giant railgun), etc.). Quality writing can be enjoyable (Bastion, Final Fantasy IV, Metro: 2033, GTA IV, in somewhat of a contradiction, Morrowind, etc.), so long as one recognizes that the game will almost certainly be a play-once-and-drop title, as if you've played it once, you've played it a hundred times. If the writing is good enough, you may go back for a playthrough in a few years, but it doesn't provide the constant, quality entertainment that other games do.