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.
Ensemble Darkhorse: Though drastically different from her OVA counterpart, TV Ifurita was apparently popular enough to be included in a radio drama taking place in OVA continuity (an alternative sequel to the second OVA), under the name of "Ifurina".
Franchise Original Sin: Makoto's status as a Chick Magnet and the accompanying harem antics. In the original OVA, they were a sidebar that provided fanservice and didn't hurt anything, but by The Alternative World, Ifurita was temporarily out of the game, the writers had completely run out of ideas, and their attempt to turn the show into a Tenchi-standardromantic comedy was probably the biggest reason that Alternative crashed so hard.
Ho Yay: Galus and Nahato, which is an disturbing example since Nahoto physically looks and sounds like a child.
Les Yay: The lesbianism in El Hazard is pretty straightforward, between Alielle and Fatora's relationship, and their repeat attempts to seduce Shayla and the others. While it's intended purposes are comedy and fanservice, it's no surpise that some viewers fail to see the humor.
The most notable instance occurs in the final episode of The Alternative World, during the trip to Arlamannote the holy spring, which the Priestesses of Mt. Moldune visit for their annual purification ritual, where they felt up Shayla, Nanami, and Afura while disguised as bath attendants. Alielle, in particular, had Afura on all fours and appeared to be humping her.
In the first episode of El Hazard 2, Fatora makes a pass at Nanami while disguised as Makoto, but Nanami saw through it, thanks to Fatora giving herself away (twicenote first by grabbing her breast, which Nanami noted Makoto wouldn't do, and because Fatora mispronouced "Shino-NO-me" as "Shino-GO-me"), and threatened to report her to Rune Venus if she ever tried it again.
The following episode has her fool Shayla, by once again pretending to be Makotonote this time, after nightfall, so Shayla wouldn't be able to make the distinction between them, in order to make out with her, thereby stealing her first kiss. The truth dawns on her when the real Makoto shows up. Shayla was justifiably pissed.
What an Idiot: In the TV Series, Nanami managed to become friends with the Bugrom and even with Queen Diva. So they will stop being evil, right? Well, that would be happening if Nanami didn't crush in front them a baby Bugrom, thinking this was just a normal insect (But don't worry, it recovered quickly.) Thus, the Bugrom locked her up and stayed evil, and that was exactly as Jinnai planned!
A lot in El Hazard 2: The Magnificent World. There are so many moments, you'd swear the cast was playing professional volleyball with the Idiot Ball. A few examples: Fatora's inability to control her libido costing the gang their money and their airship, believing Katsuhiko's obvious lies despite Nanami's warnings (keep in mind that Nanami is his sister, and would know him better than everyone else), Makoto still trying to negotiate with the Obviously Evil Kalia despite her trying to kill him mere seconds ago, the Muldoon Priestesses combining their attacks into one projectile against a character who reflects projectiles, and so on.
Ifurita even averts this. When she realizes that her projectiles have no effect on Kalia, she takes a third option and physically beats the crap out of her instead.
Jerkass Woobie: TV Jinnai, where we go a little more in depth to what makes him tick. During his childhood, everyone prefered his neighbor Makoto and his sister Nanami and he was often alone. Granted, his Jerk Ass nature still means he brings it on himself, but in some ways this makes his situation somewhat more understandable.