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The song to summon the pteranodon is a mating call. Edit
Well, it would certainly attract his attention.
Endless Ocean takes place in the same universe as the Genesis games. Edit
Coming at this from the Endless Ocean 2 angle, but consider... there has to be a way you're getting everything from a beluga to a spectacled porpoise to a river dolphin to come hang out around your subtropical island paradise, and to get them to all the locations that seem rather unsuited to their continued health. The solution? They're using the Atlantean teleport rings to follow you around.
Also, on the subject of the Song of Dragons, the song itself actually means "Asterite" in Singer. The Cavern of the Gods is built over the Asterite's home, which explains how the Commerson's dolphins and Singing Dragons are around without drowning. They're in the Asterite's sphere of influence. The Oceanides must have discovered the Asterite, and through it found a way to communicate with Singers. Also, the Commerson's dolphin you befriend is currently acting as the Asterite's liason with the rest of Singerkind after Ecco vanished into the time stream.
Arthropods hate Ecco due to genetic memories. Edit
Wonder why all the Goddamned Bats and Demonic Spiders in the 2D games are mostly arthopods? Well, according to this interview with Ed Annunziata, the Vortex gave rise to them. So, clearly, crabs, giant sea spiders, and trilobites alike remember the thrashing Ecco gave their ancestors, which explains their single-minded, furious attacks.
Ecco 3 would have consisted entirely of Ecco's Plan to save the Atlanteans and/or screw over the Vortex for good. Edit
According to the same interview linked above, Ecco didn't even bother going to the same time period the Vortex Queen did at the end of Tides of Time -- he went to the Atlanteans, who had been wiped out by the Vortex a few thousand years before the present. Perhaps he already knew the Vortex would get stomped and killed off by wildlife in Prehistory (turns out they survived just well enough to integrate into it instead), or figured any major ramifications to the timeline would have already happened the moment the Queen beat him to the Time Machine anyway, so whatever they did must have been a Stable Time Loop and it was okay to let it be for the moment. Instead, he went for reinforcements, hoping to enlist their help in taking the fight starward and wiping out the Vortex altogether.
"Big Blue" is a title, not a name. Edit
The game's a bit inconsistent, but the Big Blue is usually referred to with the definite article. Maybe in blue whale culture, the Big Blue is kind of like the king or queen, or maybe more like the global tribe elder, the oldest and wisest of a long-lived race with long memories.
Also, a Big Water is where the blue whales gather to pass on the title. This explains what a whole bunch of a normally solitary species was doing together, as well as the giant shadow below the map that comes up on sonar: that's the body of the previous Big Blue, the one from the first game.
Ecco went back in time at the end of Tides to be with the pteranodon. Edit
The Asterite is an alien seeding device. Edit
Possibly implied by the Dark Sea Word of God interview. It's the first life on Earth, the thing from which everything else spun out - perhaps the Asterite as it exists in later times is the remaining shell and mind meant to watch over the life it created, whether or not it's actually aware of this.
The Asterite sent those drones from the Vortex future. Edit
Why on Earth would the dark future Vortex Queen want to bring Ecco to her time? She's already got the last two globes, and Ecco has no way to reach her since none in his time know the secrets of swimming down the Stream of Time. So, she didn't. The Asterite managed to hide out in that timeline until it sensed its missing globes return, at which point it co-opted a couple of time-travel-capable drones and sent them back for Ecco.
Humanity is extinct by Trellia's time due to a very nasty war. Edit
If you talk to the future-dolphins, some of them tell you that "The floating islands were born of the great eruptions." These 'great eruptions' were nuclear warheads or something equally devastating, and the floating islands were shelters humans made. Singerkind understanding of these events is vague at best even for what count as the history scholars among them.
The Asterite is the ocean's mind in the good future. Edit
"The ocean is alive now - it feels and thinks." The Asterite's has become its brain, and the water is its extended body. That's also where the Skyway came from - it wants its Singer friends to be able to travel anywhere, even the ones that can't fly.
Endless Ocean takes place in the same universe as Defender. Edit
Similar to an above theory, only for the Dreamcast/Play Station 2 game as opposed to the Genesis series. The player character's interactions with the various cetaceans are the first sparks of the alliance between Singers and Humans. Endless Ocean 2 is where the more in-depth interaction starts, with ambassadors from different dolphin species guiding the player to better understand Singer culture, showing them the remnants of a previous alliance with the Okeanides, which ultimately fell to ruin for reasons as-of-yet unrevealed (possibly falling apart after fending off an earlier Foe attack, in which they were victorious but with too many losses to continue their culture). The Commerson's dolphin is the final guide, implied to be able to speak and guarding the ancient treasures alongside the singing dragons. Basically, the player in the Endless Ocean games is responsible for the start of the utopian society spoken of at the beginning of Defender.
And just to add to the fun, Ecco is descended from the albino bottlenose dolphin that the player partnered with, defending the utopian human/dolphin society because his line is ever-grateful to the race that rescued their ancestor from sharks. The great white shark in the second level is a descendant of either Magu Tapah or Thanatos - or, if you believe him to be an immortal ocean spirit, is Magu Tapah. The eight-arms is a friend of the giant squid (both guarding the entrance of caves - and who knows how long giant octopodes/squid can live?), and the humpback whale mother and child at the beginning of Defender are the several-times-great-grandchildren of the humpback whale mother and child towards the beginning of Endless Ocean 2.
The famous all-N's password was a plant. Edit
As you might know, if you put in the password "NNNNNNNN" in the first Ecco the Dolphin, you'll be transported to everyone's favourite level, "Welcome to the Machine". I suspect the programmers knowingly planted that one, for "NNNNNNNN!" is the sound most players will soon be making upon arrival.