Mega Man Legends/WMG

Mega Man Legends is set in the far future of Laputa: Castle in the Sky

Laputa is a base of the "true humans" of Mega Man Legends who wanted to live closer to earth instead of the Elysium satellite but eventually started rejoining with the "carbons". This still makes the statement that no true humans are left true as, save for the ones in Mega Man Legends 2, they mixed with the Carbons.

There are a lot of similarities between both:

Shiny crystals that can make things fly - check
Strange flying machines that could double as ships - check
Character designs - check (OK both are Anime, they're still similar enough to count)
The designs of the "ruins" in Mega Man Legends and Laputa in Laputa: Castle in the Sky - check
A "ascended" kind of humans that vanished - check
Lost technology - check
Ancient weapons that can wipe out whole civilizations - check
A artificial weather anomaly that can hide a entire island - check

But what personally is a example is the design of the Boss in the lake ruin of Mega Man Legends which looks somewhat similar to the robots guarding Laputa.

Dr.Wily is the Bonne family's ancestor

It would explain the Skull symbol.

Biggest problem with this: Nobody in the MML world is actually human any more, so he can't be their biological ancestor.
- Depends how we view this though. Wily considers Zero(His final creation) his son for example.
- Given that there's a boat owner named Wily, Wily is a surname, and that the owner in question looks just like ol' Albert, its pretty damn clear that even if his genes aren't around anymore, somebody made sure something of Dr. Albert Wily would exist in the Carbon genepool. Or whatever they have instead of genes to pass on traits. One of the initial Carbons was probably modeled after Wily as closely as possible, most likely because the designer thought it'd be a good design for robotics assistants.

Volnutt was "Joe"'s last name.

Both Roll and Barrel have the surname Casket, but it's established that Barrel is Roll's grandfather on her mom's side. This troper recalls hearing somewhere that sometimes in families where the mother still uses her maiden name, that name will be inherited by her daughters while sons get the father's name. Since Megaman was raised as Roll's brother, he was given her father's surname.

The last human DNA

So it's established at the end of Legends 1 that Megaman Trigger contains the last remaining human DNA. In a hypothetical third game (sixth, if you want to get technical) it's entirely possible that the main quest results in the replication of this DNA. As Megaman, Roll and Barrel gather round what looks like a Doctor Light capsule, the door slowly hisses open. And out steps... Wily. Cue 8-bit flashback cutscene of Wily replacing Light's DNA sample with his own. The newly reborn Wily creates chaos, and Megaman is forced to decide... destroy the last traces of humanity to preserve civilization as he knows it... or allow humanity to be reborn, with Wily as its blueprint?

That is AWESOME.
Agreed, when they start taking suggestions in the Dev Room at Megaman Legends 3 Project blog, please send that idea in.
- Sent, I hope.

The vault Mega Man Juno was hibernating in is a robot construction chamber

How else was his backup data going to 1. get a new body, and 2. get back in the Main Gate? Okay, there's Eden, but then he'd have to take the long route.

There will be a level in the third game where you (playing as Mega Man Volnutt-Trigger) carry out the mission to destroy elysium

This one pretty much explains itself.

- Horribly Jossed.

Mega Man Legends 3 WILL be uncancelled...

...only for it to be released as a crappy game with all fan-made characters acting like total idiots, due to the fans' outrage.

The setting is due to someone replicating/reactivating a plan set by Master Thomas.

He did say he wanted to reset the world, didn't he?

If it's ever released, in Mega Man Legends 3 Mega Man Trigger will find a Dr. Light capsule

And it will know of his existence.

Fisherman/Marina Wily really is Dr. Wily

Come on, he was a bit too interested in the knowledge that the Bonnes built a robot out of the wreckage of his ships. Evil chin rub of doom and everything!