Contested Sequel: This season is divisive, primarily because this is the first series that steps away from magical girl elements and toward a more military setting, but also because some characters are pushed aside in favor of new ones, Yuuno and Chrono being among the most frequently mentioned. It also doesn't help that the girls are aged up and the setting has moved off of Earth, ensuring that there is very little of the familiar to fall back on. Some long-time fans dislike the changes, while others are more fond of them.
It wasn't uncommon after StrikerS to ship Vivio with Lutecia (the only other person remotely close to Vivio in age who wasn't related to her in some way) or to age Vivio up and pair her with Hayate (most likely because Hayate is one of the few main characters without a 100% confirmed ship). This has died down a lot nowadays thanks to ViVid since now most everyone tends to ship her with Einhart.
It's not uncommon in some fan works with Ginga to either ship her with Fate or at the very least insinuate that she has a crush on her most likely thanks to Fate rescuing her when she was younger. It is downplayed however since Ginga wasn't that much younger then Fate when she was rescued and it's very likely the two would work together on cases so a romance is possible.
The TV version of the "White Devil Incident" in episode eight of StrikerS made a lot of people think that Nanoha had some sort of Post Traumatic Stress Syndrome from the timeskip between A's and StrikerS and that her reaction to Subaru and Teana's dangerous tactics in the mock battle made it look as if she wasn't fit to be training the two. The DVD version of the situation helped clear up any misgivings. She had more of a "disappointed parent" look on her face than the more Higurashi-like look in the TV version.
Just before her legendary attack in episode 25, she stomps on the floor, possibly to brace herself, but more likely simply because of how badass it makes her look. In the TV version, some dust is kicked up when her foot pounds onto the floor. On DVD that part of the floor is destroyed. Inexplicably, many people seem to prefer the second.
Various examples of QUALITY animation are fixed in the DVD releases as well.
Cinque of the Numbers is fairly popular, despite only appearing in three episodes and being the only one absent from the final battle. It helps that her design is interesting, she has cool powers and she's a loving older sister who, despite having the longest sentence of the reformed Numbers, insists on atoning for her crimes for her younger sisters' sake.
Despite - or perhaps because of - her incredibly minor status, Sette gained a bit of popularity in some fanfiction circles. One popular topic is to expand on her fate - she is not in rehabilitation like the rest of the younger Numbers, but appears to be treated as less of a criminal than the older imprisoned Numbers, leaving open the possibility of her release.
Hilarious in Hindsight: Lutecia Alpine's fan nickname ("Loli-Rider") now qualifies as this due to the Babylonia chapter of Fate/Grand Order releasing a younger version of Medusa under the Lancer class who looks almost exactly like her.
Moe: Reinforce II, Vivio and the younger Subaru seen in flashbacks. Even Adult Nanoha still qualifies as this.
Moral Event Horizon: Quattro crosses this when she brutally tortures Vivio and insults her mother Nanoha right in her face. If she didn't cross it then, she definitely did when she forced Nanoha and Vivio to fight each other. Especially with her line, "Now kill each other, like a good mother and daughter".
Nanoha's Blood Knight reputation was already around by the time of A's, but after her abortive brawl with Signum in the manga there was no going back.note Note that this is a coloured and enlarged, but otherwise completely unaltered panel from the canon StrikerS manga.
Subaru was already seen by many as Ambiguously Gay, but the opening scene of episode 10 pretty much solidified it. She tries to wake Teana up by climbing into her bed, straddling her, and squeezing her breasts for several moments, all with a distinctly un-innocent expression on her face.
Slow-Paced Beginning: The show is slow for the first ten episodes, focusing on training the new foursome and not very impressive battles against generic robots. Then Vivio comes along, and the plot and action kick in with force.
Straw Man Has A Point: Regius is one of the few people who distrusts Hayate for her criminal past, and even Auris suggests that he keep his opinions to himself. While the viewers and those close to her know she did nothing wrong during the Book of Darkness incident, he and much of the rest of the Bureau apparently heard a version of events in which Hayate accepted full responsibility, making his distrust seem more logical if ultimately incorrect.
Nanoha's near-death experience is very underplayed, although the belief that something like that might happen again is why she is hesitant to adopt Vivio at first, and she later resolves to make sure it does not happen again for Vivio's sake.
Regius's distrust could have segued into political intrigue and been expanded, but gets forgotten about very quickly.
Throughout the season, there is an obvious implicit comparison between Nanoha, Fate and Hayate and the "Three Legendary Admirals" who built up the TSAB — with the tantalizing possibility that they would become the ruling forces for the Conspiracy Redemption. This idea ends up left completely unexplored in post-series material, perhaps because it would have interfered with Magical Record Lyrical Nanoha Force.
Earlier episodes go to some effort to build up Nove as a significant character, introducing her before any of the other Numbers besides Uno, and with Face Framed in Shadow in order (one supposes) to foreshadow her resemblance to Subaru. In the end, however, this goes nowhere — said resemblance is never remarked on by anyone, nor is the fact that Nove is based on Quint's DNAmentioned at all in the anime. One gets the impression that the writers intended this as a subplot, only to end up abandoning it due to time constraints. Which is arguably a shame, since Nove being instrumental in wounding and abducting Ginga could have had an extra poignancy, as could her subsequent grudge against Subaru. Teana's implied comparison of Nove to Subaru in episode 24 would also have been much more meaningful if this subplot had survived.
On a more abstract note, all of the major events that have happened off-screen between A's and StrikerS. Nanoha, Fate, and Hayate getting to truly know each other after the Book of Darkness incident, the three of them formally joining the TSAB and their rise through the ranks, their move to Mid-Childa and the tearful farewells with those they left behind on Earth, and of course Nanoha's accident. Between all of that, there's at least an entire season's worth of story that was completely skipped.
Vivio and Lutecia was a not uncommon fan pairing, at least pre ViVid.
Viewer Gender Confusion: Otto. Female, for the record. This is compounded by her use of the masculine pronoun "boku", and the fact that many of her fellow Numbers are unsure of her gender.
Agito. The poor thing was used as a lab rat by mysterious scientist and it was almost completely broken when Zest and Lutecia rescued her. She recovered her enthusiasm and becomes a loyal Unison Device to Zest only to see him die at Signum's hands. Agito was taken under Signum's wing and they started to slowly develop close bonds and the little redhead eventually grow genuine feelings for the Blazing General. Came FORCE and she witness how Signum is near killed in front of her eyes while she's unable to do anything to help her beloved master. Life has been pretty harsh on this little device.
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