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.
It Was His Sled: The Vortex aliens and time-traveling shenanigans were meant to be enormous twists in the first game that undoubtedly caught a lot of gamers by surprise. Nowadays, it's impossible to talk about the series without mentioning either.
Most Annoying Sound: Ecco's sound bytes when he is injured in the first game is short but grating on the ears, especially when you get hit by enemies and hazards multiple times in a row. The sequel changes the sound to a more quiet like chirp/squeak.
The sudden loud noise of the Vortex sequence when Ecco's pod is taken. Talk about startling...
Nightmare Retardant: Some of the enemies are just still pictures ramming into Ecco. It kind of takes the fear of getting swarmed by giant crabs out and ruins the immersion.
Paranoia Fuel: So you've just started Tides of Time. You're zooming around one of the first levels, enjoying the better controls, and suddenly you see a terrifying mass of blue chitin that kills you instantly. It was one of the alien enemies in the first game that you never saw till the last level. On the one fin you don't want to go that fast ever again in case more of them are floating around, but on the other...you have to. Eep.
In Defender, seeing another dolphin usually indicated an area that was relatively safe, and promised conversation with an ally (or at least someone who wasn't actively aggressive). Then the Dolphin's Nightmare stages come along, and any time you see a dolphin swimming in the distance it might be just another friend... or someone out for your blood.
Porting Disaster: The GameGear version of Tides. It is now thought it was based on a prototype of the Genesis/Mega Drive game. The Game Boy Advance port of the original Ecco isn't quite so atrocious, but removed almost the entire soundtrack, replacing it with a 30-second loop heard during the time travel sequences in the original game.
Scrappy Mechanic: The starfish you have to echolocate over to rocks so they can smash them. On the plus side, they wreck any enemies in the way, but it can be quite tricky to get into the proper position, and if you take too long between calls, they disappear and you have to start over.
That One Boss: Given the general difficulty almost all the bosses are well-hated, but the final boss of the first game deserves special mention. She actually isn't all that bad herself, but if you die you have to pick your way through Welcome to the Machine again. Worse, she has a move that will kill you instantly or even freeze the game forever if you have infinite life.
The Foe Queen in Defender deserves some elaboration. Five minutes before she kills you by leaking her own blood. Scary as fuck background music, as you get to hear the increasingly violent beating of her heart as you kill her. And the level is dark and cramped, because you're inside her body.
That One Level: Every game has at least one. Inevitable given the general difficulty, really.
Ecco the Dolphin features Welcome to the Machine: Five minutes of twisting, turning, auto-scrolling Hell. And just to make things even better, if you lose to the final boss you get to go through again!
The Japanese release attempts to ease the frustration by adding a level called "The Stomach". This level is gotten to by being swallowed by the Queen; while you are still in danger, you don't have to go through the machine to get back to fighting her.
The Hanging Waters levels in Defender of the Future, and by proxy the Skyway in Tides, can vary depending on the player. They're insanely hard, but both are some of the most beautiful things to come out of their respective consoles.
The Woobie: Ecco himself is a Stoic Woobie, particularly in the first game, where he's kicked into a globe-spanning adventure when his family is suddenly stolen from him by terrible, powerful forces he can't begin to understand.
In the Dolphins' Nightmare section, a pair of enslaved humpback whales provide the power for the Hanging Waters, a process that shortens their lives each time it's initiated. They're so amazed to meet a dolphin that's not abusive towards them, they willingly go through with it to help Ecco out.
Also in Defender, the Outcast dolphins come across as Jerkass Woobies. Yeah, they're bastards to the other marine life, too, but they're still, well, outcasts, and the Clan likes to cut off their food supplies and sic sharks on them for giggles.
Pretty much all the dolphins from Man's Nightmare. They aren't as intelligent as dolphins in the true timeline, so mankind took advantage of them and enslaved them. Then humans wiped themselves out, or from the dolphins' perspective, disappeared. The Mover (hard-labor class) dolphins were happy about this since they no longer had to work endlessly, while the Circle (machine operators) dolphins refused to give up their tasks in case man showed up again, and the Crimson (lore-keepers) pined for the loss and wondered if man was testing them, and in the meantime they forgot where to stain their fins red, so this class has all but died out (though Ecco rediscovers it and stains his own fins, which makes the last Crimson very happy). So basically, all the dolphins are living in a post-apocalyptic wasteland they didn't create, don't have the intelligence to improve their situation, and have no clue where their masters got to - or whether life would get better or worse if they came back.