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: Kakashi promised to become Naruto's sensei, but was distant to him because Naruto looks like his parents. He becomes less distant (and more possessive) when someone else gets the position. This ACI recurrs in several of Lucillia's fanfics, too.
Broken Base: To a degree, FT:S got hit with this thanks to Sasuke's sperm-donor children, which is unsurprising considering how controversial the Uchiha Clan are in Canon.
Ensemble Darkhorse: Dare I say that the Shimura family qualifies? After all, Tetsuo is a really good teacher and a Rounded Character despite being an OC, and Danzo, while not necessarily a "good" guy, is admirable because of his Manipulative Bastardry - you can like the old man whilst still recognising how ruthless he's capable of being.
Fridge Horror: In Team Tetsuo, Hiruzen discovered that the Academy was being sabotaged when Naruto and his team were reviewing their history. Which means that the sabotage still continues from Team 7 to Shippuden and won't be found out until it's too late.
It's not "Fridge" anymore - in Chapter 4 of Shippuden, Sakura notes how much less competent the younger ninja recruits are than even her own peers, but because the curriculum isn't that different from her own time as an Academy student (only over 3 years ago), she hasn't realised that it's the cause of decaying standards
Growing the Beard: The original First Try was a well-constructed story, but suffers partially from lack of focus on team relations and being over very quickly (the side stories do a good job of remedying this). First Try: Team 7 improves by being longer and having more focus on these faults. However, the fandom appears to be in universal agreement that Team Tetsuo is where the series truly exhibits beard growth - a proper break from The Stations of the Canon, Character Development galore, original plotlines and themes, and arguably an even better story than the primary First Try story plot (it certainly seems to be the most popular). Many fans consider it part of the Main Series even though by label it's only a Spin-Off.
Jossed: When First Try: Shippuden was started, Lucillia interpreted Tobi as an ousted Uchiha whose wife and children were killed by his clan for being foreign-born and illegimate. Seeing Tobi is actually Obito Uchiha, Lucillia intends to rewrite FT:S to fit The Reveal, but she doesn't want to abandon the plot about the Uchiha Clan murdering illegitimate children - Itachi even references the practice when talking to Kisame in Team Tetsuo.
It has since been revealed that Tobi is a name which multiple Uchiha who follow Madara take up, hiding under the same mask with the pretence of being one person rather than multiple. Besides Obito, there is only one Tobi left - a much older man who lost his extended family due to the Uchiha Clan murdering them, for which he paid them back tenfold (literally, as a he took at least ten Uchiha lives for each of the loved ones they killed).
It should be noted that Lucillia implements Orwellian Retcon when it suits her, especially if she can edit the plot without damaging her overall story. For instance, the original First Try was written before The Reveal that Tobi wasn't Madara came out - this necessitated the editing of a scene which explicitly identified the two as being the same individual (though she waited until The Reveal of who he actually is to do so).
Magnificent Bastard: Danzo, who turns Barako's gossip campaign against his grandson against her by telling nothing but the truth.
Tearjerker: In FT:S, when gambling takes over Satoshi's life and Naruto tries to hold an intervention, but fails.