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.
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.
Magnificent Bastard: Ghaleon, manipulating the heroes for their own good right under Zophar's nose.
Needs More Love: Silver Star got THREE remakes, while poor Eternal Blue only got two, and one of them never left Japan! While US gamers can still find Eternal Blue Complete if they look hard enough (not to mention be willing to drop some serious coin), those PS1 cd's aren't gonna last forever!
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.
Porting Disaster: 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 significant quality loss. Even the Sega CD version sounds like an orchestral arrange album in comparison.
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.
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. One of his attacks hits the whole party, others can drain HP and MP, and he can also heal himself. He has a buttload of HP, and each hand of his has different weaknesses and abilities. Before you start the second form properly you have to spend 5 turns defending until you're able to damage him. And both forms have unskippable, lengthy cutscenes in between them.
They Changed It, Now It Sucks: The remake, despite its often very good additions to the story, is not proportionally as good as the "16-bit masterpiece" that is the Sega CD original. Long-time fans tend to prefer the older version.
Furthermore, 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.