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: Hinted at by Word of God. Big BadWilhelm's plot involves resetting time over and over again to avoid the universe's eventual destruction. The characters argue that endlessly repeating the same thing simply for the sake of existence is meaningless, and put a stop to it. At this point Wilhelm may seem like a Well-Intentioned Extremist at best and pure evil at worst (he's directly or indirectly responsible for everything that happens in the series, including each character's individual traumas), but the post-game database suggests that the party's rejection of his plan was actually what he wanted, and that by continually resetting the universe he was actually "training" the collective consciousness of humanity to move on and find a way to avoid the universe's destruction, putting him in a much more positive light.
Base Breaker: Shion, big time. For her detractors, she's obnoxious, self-centered, selfish and overall unlikable. For her defenders, she's a compelling female protagonist (in a genre where those are extremely rare to boot) who manages to stay strong despite suffering massively from Deus Angst Machina and has an engaging Character Development, which makes her very sympathetic.
Broken Base: The fanbase is broken into 3 parts with each episode. The drama with Episode II's changes was so bad, the admin of the fansite Zenosaga.com (who was the biggest fansite at the time) would ban anyone on the forums if that person defended the game.
Catharsis Factor: If Shion's behavior through the series is a source of frustration to you, you get the chance to work your issues out on her face late in the third game. Enjoy.
Evil Is Sexy: Well, sexier if you compare T-elos to KOS-MOS. "You haven't got the best of me. Hardly."
Faux Symbolism: It's difficult to tell how much is gratuitous and how much is really symbolic given the themes and plot. In general, Xenosaga is much worse about it than the Shown Their WorkXenogears, and Xenoblade, although that's because there's less of it there.
Jr.'s best weapon in I was the Blood M9, which becomes his first weapon in III because there is no equipment changing in II.
Why is Wilhelm such a good Chessmaster? Because he's already successfully implemented his cosmic reset plan at least ten and possibly hundreds of times. This means that he either knows what's going to happen (if events repeat closely/exactly) or he knows how to manipulate people to get the correct outcome (through millions of years of accumulated Batman Gambit-ing experience).
Less brilliant once you realize that like the rest of the lower domain, Wilhelm himself is reset, too. His belief that there have been many resets is an informed guess, albeit one backed up by Word of God.
At the beginning of Episode I, it's mentioned how Virgil has a condition stemming from the consumption of Realian Tissue. At the time, you're told this is treated like a kind of drug to some people, and Shion is horrified at the implications. Later, you discover that the Realian Febronia donated some of her organs to him to save his life, and then suddenly everything clicks into place.
Every iteration of Erde Kaiser. It is so powerful its a wonder the game disc in the Playstation 2 can even stay in one piece when it's summoned.
Xenosaga I had the Bravesoul and Golden Dice items which both increased attack power as the equipper's HP got lower, letting the player get a maximum of about 200% damage. The drawback of dying in one hit could be controlled with Safety Limit, which guarantees survival with 1 HP once per cast. Jr. in particular makes a joke out of every boss in the game partly due to his exclusive Dandyism, which stacks with Safety Limit and has a similar effect, but also due to the items only working with physical attacks, which he packs more of than any other character in the game.
Xenosaga III's ES battles became exponentially easier once you got your hands on the Level II Anima Awakenings, which hit most if not all mooks on the screen for ridiculous damage. You could simply charge these by walking into a battle and retreating over and over again, then firing off your BFG (or BFS) once full. Also a great way to grind for money and skill points later on.
Xenosaga III also brought you Blood Dancer, which let KOS-MOS and MOMO turn red. Then take down the final incarnation of aforementioned Erde Kaiser, itself a game breaker, singlehandedly. The reward, Erde Kaiser Sigma, who, when summoned by someone under the influence of MOMO's Magic-Attack buff, can One-Hit Kill the FINAL BOSS.
Xenosaga III tends to be filled with these. Jr. and Shion can essentially become invincible for a couple of turns via Phantom Fly, a Master Skill that allows them to evade essentially every attack in the game. While it is normally tempered by an absurdly high EP cost, there's an accessory that you can get with a relatively easy sidequest near the end of the game that reduces SP cost to 1. Add the two together, and you get either Jr. who can support with the best of them, or Shion, who can inflict reasonable damage, break, and heal. And are invincible.
Not as extreme, but for whatever reason, MOMO is ridiculously powerful in Xenosaga II. In the first dungeon, Jr, chaos, and Ziggy do around 50-100 damage. MOMO does close to 200 and never lets up as the game progresses.
A good chunk of Albedo's dialog, with Ma Belle Peche being to most notable.
Moral Event Horizon: While it has been trampled to bits by the many villains of the series, the most obvious and earliest example takes place for the character Virgil. When you meet him in the first game, he hates Realians with a passion and has even eaten their flesh in the past. He crosses the Horizon when he decides, in order to protect himself from an oncoming swarm of Gnosis, to input the Override code into some nearby Realians and then self destructs them.
Yuriev crosses it irrevocably when he uses his appearance as Gaignun to get close to Mary - and shoot her in the gut.
He crosses it again when we find out he ordered Nigredo to kill all the URTVs who survived the upcoming Miltian conflict, especially URTV 666 (Rubedo, aka Jr.) because his Red Dragon mode posed a threat to Dmitri. Plus him planning to send all the URTVs except Nigredo into the conflict in the first place knowing that it was extremely likely to cause a reaction that would incinerate the surface of the planet (killing all of his URTV children as well as every living thing on the planet) and was callously planning to use that to further his own political position.
Better: his reaction to being questioned that it was worth it to destroy Miltia if it got rid of U-DO? Yes.
Him ordering the murder of every man, woman, child, and realian on the Durandel save the four people who were useful to him.
Voyager crosses it when he murders Ziggy's/Jan's wife and adopted son.
For some, Albedo crosses it when he mind rapes MOMO.
Most Annoying Sound: Episode III: Can you people say anything besides "Ether Drive!?" Especially annoying considering each had their own saying when using spells and special attacks in I and II.
Ep. II: Mystic powers, grant me a miracle! Not helped by the incredibly bad sound recording of the line.
The footstep sounds in III are also a common complaint.
One-Scene Wonder: Orgulla is given a lot of characterization for the one boss fight you have with her and the cutscene before and after said fight, only to never be seen ever again. It's probably what made her such an Ensemble Dark Horse.
Although Patriarch Sergius XVII is the one of the primary antagonists of Episode II, he's a blip on the radar in the series as a whole.
Scrappy Mechanic: The Stock system in Episode II, which slowed down the pace of the battles to a turtle's crawl.
Shout-Out: Ziggy, and Lt. Virgil as well, look suspiciously like Rutger Hauer.
Stoic Woobie: Jin truly has a sucktacular life, on par with Shion's but keeps it all to himself. Implied to be because he doesn't want to 'burden' Shion with his own problems, as he feels partly responsible for not being able to help Shion with hers.
The Untwist: The identities of the Red and White Testaments, Kevin and Albedo, are foreshadowed with numerous heavy-handed hints and are both blindingly obvious by the end of Episode II. To smash the point home, their Episode III character art shows them both unmasked, obliterating any residual shock that would have come from The Reveal in the game itself.
They Changed It, Now It Sucks: A good deal of the problems with Episode II were the result of this. Several of the voice actors were changed, the art style was changed to a more realistic look, which is bad if you liked the old look, and the battle system was changed, probably for the worse due to the above mentioned scrappy mechanic.
What Do You Mean, It's Not Symbolic?: Nephilim's necklace is in the shape of a cross, her name is a direct reference to the giants from the Bible who created the Great Flood... let's not get started on the symbolism behind the white and her possible relation to Elly.