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.
Alternate Character Interpretation: This series has a very controversial one of the Jedi Order. The Jedi Knights have severed themselves from their families and made use of a slave army in order to protect a Republic that's obviously not worth protecting. As a result, they're individuals who deserve nothing but scorn and derision.
Amusingly, fans have a similar view of the Mandalorians, treating them as essentially psychotic killers under the control of a Villain Protagonist.
... which is a perfectly valid interpretation. Much as the attitudes of the Mandalorian POV characters might obscure it, Traviss shows them doing plenty of nasty things.
Skirata reflects on this in Order 66 and calls his motley crew his "syndicate." He thinks what they are doing is completely justified because they are saving millions of lives. He may be right, he may be wrong.
That is the entire point of the Republic Commando series. These are not Jedi seen through the eyes of Jedi, or Jedi seen through the eyes of normal civilians and the like; these are Jedi seen through the eyes of the MANDOLORIANS. Traviss' books are a viewpoint of how the Mandalorians see the Jedi Order, and those raised by Mandalorians.
Which was fine when Traviss was writing from Mandalorian and Mandalorian-trained Clone Troopers perspectives, except quite often she was guilty of having non-Mandalorian characters agree with or hold perspectives they absolutely shouldn't. Etain and Bardan were practically written so Traviss would have Jedi who agree with her incorrect assertions regarding the Order and its practices. In the twenty-plus thousand years the Jedi Order has been in existence it has always required parental permission to take children for Jedi training, and yet Etain, a trained Jedi, breaks down in the belief the Order will steal her child from her.
Internet Backdraft: Whatever SW forums you visit, don't mention Traviss. It can and will get ugly.
Fan Hater: Traviss is a notorious one of these towards the Jedi. YMMV on whether it is justified or not.
Fridge Horror: Season Six of The Clone Wars revealed what Order 66 really is: a physical chip inside the head of every clone that drives them to kill Jedi against their will. In other words, in the official setting, it could very well not have been a Jedi who kills Etain when she attempts to protect a clone soldier, but Darman and Omega Squad, who would be forced to kill her via Order 66 and the implant, if they could not resist it.
It Was His Sled: Sev's fate at the end of Order 66 due to the games coming out earlier. It'll still wrench your heart, though.
Somewhat justified. Sadly Traviss rage-quit when she was going to subject her own creation to some very well deserved scrutiny. There was much foreshadowing in 501st that even the "safe harbor" on Mandalore (the planet) may not come free and without attachments. Mand'alore (the ruler) is just as political as the rest of the galaxy and would use the clones for his own "patriotic" purposes.
Marty Stu: Skirata, arguably. He is a father to his men and all of them love him. He is their patriarchal role model and he can do no wrong. He will do anything and everything to ensure his boys get the life that was taken away from them. Skirata even lets Darman beat the crap out of him for not telling him about Kad.
That said, Skirata does make some rather egregious errors of judgement, including the aforementioned failing to tell Darman about his son. He is also a psychological mess; it is pointed out by several Jedi that Skirata is practically swimming in rage, guilt, and self-loathing.
Mis-blamed: Whatever the series' faults, the 3 million clone troopers number wasn't one of them. That blame lies at the feet of RA Salvatore's Attack of the Clonesnovelization, movie-level canon which interpreted Kaminoan Prime Minister Lama Su's line, "200,000 units are ready, with a million more well on the way," as meaning 200,000 clones rather than a more sensible 200,000 military units. Karen Traviss and others had no choice but to use it because, at the time, movie canon overrode EU novels.
Moral Event Horizon: Scorch views a mortar attack on a base's commissary as this. When he and the rest of Delta tracks down the guys that did it, he brutally kills them, then repeatedly pours blaster bolts into their bodies in full view of a gaggle of onlookers.
Squick: The clones are only 10-13 years old in the books. No matter how many times the book stresses they are men and mentally and physically twice their age, there is no changing the fact that the clones have only been in the galaxy for 10-13 standard years.
But that is the thing: the clones may be 10-13 years old by the standards of normal Humans, but they are still physically and mentally adults. They simply lack the experience normal adults would have because of their accelerated age and the focus of their lives on training for a war they were bred for.
They Wasted a Perfectly Good Plot: The storyline takes place during the same time period as the Mandalorian Protectors are supposed to be rampaging through the galaxy, even launching an attack on the clone's homeworld of Kamino. Do we get to see some more Mandalorian versus clone action? Nope. Do we even get a cursory run-through of the campaign? Nope. And by the last books, our protagonists are regularly teaming up with the last survivors of the Protectors without any tension about the whole "attacking our little brothers," or "wiping out almost everyone we fought alongside."
The Woobie: Etain pulls this off surprisingly well. Right up until she dies trying to save clones who would have killed her had she realized what was going on.Actually, all of the clone troopers pull this off to some degree, especially Atin, who blames himself for his squads' death. He's the only survivor of his squad TWICE.