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Regardless of if you go with the Creature Cards idea or not, I think the game should have some special creatures that the player has to unlock by doing something in the game (and not something they can just pay to unlock through DLC or Creature Cards). It doesn't need to be tied to specific events in the story. Kind of like how in old fighting games you have to achieve special requirements to unlock certain characters. Something to keep in mind about unlockable content is that the reward should be worth it. Like how in some RPGs you only get the ultimate equipment by beating the bonus dungeon in the post game, at which point the reward serves absolutely no purpose because you've already done everything in the game.
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This post is somewhat silly in nature, but for your Leviathans and other giant sea creatures, will you be drawing some inspiration from giant monster (kaiju) movies? They don't need to have super powers like energy beams, but I would like to see some imaginative designs beyond the usual generic oversized and mutated everyday creatures we see in other media. When I was a kid, I always liked the outlandish designs in giant monster movies.
Since "everything wants to eat you", if you ever have to fight the giant creatures, you could also take inspiration from survival horror games, some of which have enemies that you can not defeat and must run from. Too many games lull the player into a sense of security and empowerment because absolutely everything can be defeated in some manner.
Something else to keep in mind about fighting giant creatures, if you want them to be beatable, is that they have to have some sort of achilles' heel. This is another place to show off creativity as there are better ways of going about it other than waiting for an opening in the attack pattern or looking for the glowing spot on the body and pressing "attack".
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Since animals dream just like we do, you could use that as part of the storytelling. It would be awesome if the game featured ominous and surreal dreams.
Soul Blader imagined what plants and animals might dream about, but I haven't seen it examined in any other games. It could be something to make LB stand out.
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Bobbit worms would make horrifying enemies. Were they those "arm" enemies in Ecco that grabbed you?
This is a video of a Finless Porpoise in an aquarium. They're surprisingly agile for barely having a dorsal fin. http://www.youtube.com/watch?v=yjRCtTn1q9w
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For your imaginary creatures, will you perhaps use charts in the Creature Guide to show how they evolved?
Sorry to stretch the thread with another image, but something like this is what I'm talking about. I find it much easier to understand when I can visualize it, instead of just reading about how "cetaceans evolved from mammals that moved into the water", which can make me think of any medium to large sized mammal.
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The arm enemies in Ecco were called Leeches I believe...though no one knows what they were truly based off (and also they didn't hurt you like that thing looks like it would). Maybe Ed could step in here.
If we want to keep these games realistic we can't go towards the "giant monster movies" approach. Sea serpents and leviathans should draw more realistic inspiration than anything else, keep them real. As for weapons, they could use a sonar of some kind. I usually feature sea serpents in my stories as creatures with a sort of pulsar sonar that is both a little electrical and is loud enough to stun creatures. We don't need a godzilla :)