Complete Monster: Zophar is the self-styled lord of darkness and the one responsible for the Blue Star being stripped of all life. As we see in flashbacks, Zophar led a campaign of conquest on the Blue Star that only ended when his arch-nemesis, the goddess Althena, was forced to seal him at the cost of all life on the world. Even through his prison, Zophar reached out to corrupt mortals, twisting the church of Althena into a Corrupt Church that was responsible for centuries of suffering and cruelty. Zophar excels in twisting and corrupting hearts to even turned loved ones against one another, and unlike most dark lords, Zophar fully understands goodness and righteousness enough to exploit it: manipulating heroine Lucia's love for her friends so she wouldn't have the will to destroy him at cost of the world. Zophar takes her captive to use her powers to remake the world in his twisted image, not caring about the death toll. When he decides the world is too much trouble, Zophar merely elects to destroy it utterly with every living soul.
Epileptic Trees: Fertile ground for these thanks to the Left Hangingsequel hooks. The relationship between Althena and Lucia, the nature of the Blue Star, the nature of Althena, Lucia and Zophar, and just who built the infrastructure connecting the Blue Star and Lunar - all popular topics. Unless Lunar 3 comes along any time soon, these questions may never be answered.
Lucia really has to be noted here in particular because there are so many theories around her. Okay, she isn't "human"... so what the hell is she? An "enhanced human"? A demigod? An actual god? Althena's sister? Daughter? Something else? Naturally, there's room for all of these interpretations and more.
Even Better Sequel: Lunar: The Silver Star was a charming if somewhat derivative JRPG with memorable characters and a fun story. Eternal Blue, however, improves upon the game in almost every way with a more mature storyline, better developed characters, a better soundtrack, and an improved menu system that does away with the more cumbersome aspects of Silver Star Story's system.
It's also worth pointing out that Zophar says to Ghaleon, "Use what's left of your head," at one point in the Playstation remake. Puts that patch of scales on his face in a whole new light.
Magnificent Bastard: Ghaleon, manipulating the heroes for their own good right under Zophar's nose.
Periphery Demographic: As pointed out in the "Making of Lunar 2 Eternal Blue Complete" CD, more girls showed up than guys at an event to meet the creators in Japan, much to their surprise.
Worth noting is that there was a shoujo manga adaptation of the game, told from Lucia's perspective. This may have done a lot to increase the game's popularity with girls.
Porting Disaster: Not a particularly egregious example, but the PlayStation remake was a port from Sega Saturn, and the conversion left it a bit worse for wear - particularly in terms of audio. The background music was converted into a MIDI-like format during porting, with a noticeable decrease in quality (though it still sounds quite good on its own). The Sega CD version, on the other hand, used Red Book audio and sounds a bit more natural (although the actual sound quality leaves a lot to be desired).
Scrappy Mechanic: In the English localization of the Sega CD original, you had to spend magic points earned in battle, usually reserved for upgrading your skills, to save. Working Designs thought it would add more "risk" to the game's save-anywhere mechanic.
The translation itself - at the time, a lot of translations were simple literal translations, sometimes with a "Blind Idiot" Translation thrown in here and there with proofreading being somewhat limited. Working Designs was one of the first companies to attempt to produce a more cultural translation, change sentences around (so they made more sense), removed jokes and references that would confuse American viewers, and change NPC dialogue around so they had more to say. What would have been a Woosleyism in the 1990s wouldn't exactly fly today.
That One Boss: Borgan in Eternal Blue. He has a spell that, if cast twice without healing, results in a Total Party Kill. And he's fast enough that you couldn't be guaranteed a chance to reactively heal in between castings, nor did you have the MP to toss out the healing constantly. This was only in the SegaCD version, though. The remake toned down both his speed and damage to the point where he became an Anti-Climax Boss to anyone who'd played the original. In the original version he's the fight that gives people the most trouble.
While Borgan was underwhelming in Eternal Blue Complete, his companion "dragon" (the Black Fiend) ascends to That One Boss status in his place through sheer annoyance. Its speed can beat out Jean (the party's fastest character), and its favorite move, an Affect-All MP drain, tends to "suddenly" (read: only for this attack) be that fast every time. And to top it off, the best defense against this, White Dragon Protect, costs a whopping 60 MP, and is best equipped on Jean, forcing one of your best attackers into a defender/support role. You're in for a long fight.
The Fake Althena fight is like this too. Either you are at a slightly high level for the time of the fight (I was a couple levels lower because I didn't feel like fighting every fight in the rather long dungeon before this fight), and thus have enough firepower to win the fight before this attack happens, or you have to cast White Dragon Protect the turn before a happens—meaning you're either using a guide or you have already been killed by it once. Not sure if defend would work quickly enough to save you, but if it did you'd probably get overwhelmed in trying to recover anyway.
Zophar; even by Final Boss standards he's ridiculously tough in both versions. His first form isn't so bad, but his final form scrunches your party members into an enclosed space so area attacks affect multiple members, he gets around 4-6 attacks per round via his separate hands, is insanely fast, and if you kill one of his hands or take awhile in fighting him, he gets angry and can do an attack which hits for over 7000 damage when your max HP is 999, but in the remake you pretty much need to do that because one of his hands heals the other and his main body. One of his attacks hits the whole party, others can drain HP and MP, and he can also heal himself. All of his parts have a load of HP (in the original, they have as much his body), and each hand has different weaknesses and abilities. Before you start the second form properly you have to fight the invulnerable first form. Both forms have unskippable, lengthy cutscenes in between them. note Instead of defending for 5 turns, you're better off going all-out on the two hands that aren't shielded during that portion of the fight. With a bit of effort 2 of his 4 hands can be destroyed before the third phase of the fight starts, making it just a little bit more managable. Since Lucia restores all your HP and MP when the second phase ends, you don't need to hold back anyway.
They Changed It, Now It Sucks: The remake, despite its often very good additions to the story, gets flack from some long-time Lunar fans for the plot details that were cut from the Sega CD original.
The English translations of the two versions were done in a slightly different style; many people thought that Working Designs went overboard with the jokes and pop culture references, so they toned it down for the remake. YMMV on which version is better.