So chiggity check this out.
I've done some extensive 'research', AKA, forcing myself to play through the entirety of Journey of Dreams and then easing my burning hatred for Sonic Team by playing into Dreams, and have come to a conclusion; NiGHTS Journey of Dreams takes place before NiGHTS into Dreams.
Ok, so the first change is obvious, Will and Helen's town (offical name BTW, what a way to show dedication to your craft) has old styled, elegant, mid-early 1900's European architecture, whereas Twin Seeds has futuristic, 90s-licious buildings and houses. Another thing I noticed was that Will's house (seen in his intro) looks very similar to Claris's house, and it may be a stretch, but what if Will and Helen got married way down the line, and when he died, he inherited the family home. They remodel the house, and have a baby girl, who they name Claris.
Here are some side notes I took when I wasn't writhing in pain while playing JoD:
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Owl: I’ve been here since long before you were born- gonna have to get a bit edgy here, but if Owl has pretty much always been in Nightopia, you'd think he'd be hanging around with his annoyingly paced dialogue and phoned in voice acting in NiD. A maren probably killed him, and I don't blame said maren. Wouldn't actually surprise me if it was NiGHTS, even.
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Reala: Where’s your persona mask? Took it off again, didn’t you?- Reala acts as if NiGHTS has only recently rebelled
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NiGHTS has to explain dualizing, and does it slowly and awkwardly, in NiD she seems used to it. She makes a face of content/pleasure when dualizing the first time in JoD, suggesting that it's a new high for her.
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Wizeman seems to have done away with the persona masks
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The physical dream gate seems to have been completely destroyed or taken over by Wizeman in NiD
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In JoD, dreamers just sort of lose all their ideya on the way to the dream gate, and in NiD, marens just steal them directly. They're then put in holding while waiting to be taken by a higher-up Maren or even Wizeman, which is far more efficient than having to search for them in the void between the waking world and Nightopia
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Reala just sort of gives the keys to the cages to quicc marens, like a fool. He realizes he shouldn't have done that in NiD, and just drags NiGHTS to the nearest Ideya palaces after she escapes.