Mega Man Battle Network/WMG

Colonel.EXE is an E-rated representation of a hermaphrodite.
First, look at his appearance. Not only does Colonel wear semi-feminine attire, Colonel also has, what appears to be, breasts and hips. Now, here's the second piece of evidence: Iris, Colonel's emotion data and "sister". Now, this may seem non-canon to you, but Iris isn't his sister, because, unlike the Mega Man X counterpart, Iris was actually inside of him. Colonel's personality change without Iris is actually symbolism for what an outwardly male hermaphrodite has to do in order to fit in: act completely male in order to fit in. The manga holds some evidence, too: the first with Colonel stating that he and Iris were the same people, and him saying that Serenade was "the only one who could understand him". Since Serenade is also hermaphrodite, Colonel might be saying that most people don't know what it's like to feel like you're born in a different body. The reason people call Iris Colonel's "sister"? The Western fans feel uncomfortable with the issue of hermaphroditism, so they just portray Colonel and Iris as siblings.

MMBN takes place in a dystopian world with no Internet freedoms.
MMBN takes place in a dystopian future/alternate reality, where the RIAA wins and torrents are punishable with thousands of e-dollars in fines. The law is upheld so fiercely that the mere mention of downloading a chip, subchip, .MP3 or .txt file is met not necessarily with outright deletion, but incredibly heavy and imposing restrictions or fines, since everyday life has become so ingrained to the internet that even the stove is online.

This is why individual homepages are blocked by those security blocks - PC privacy is still upheld as a law, so only the most trusted of friends can enter their homepages, which prevents the Officials from searching their hard drives without a valid warrant.

The Undernet is the only reliable place to download illegal wares, and as such, it is artificially dangerous - it's a security measure to keep the Officials from snooping around their servers. The Undernet is seen as a lawless hive for the most degenerate of users, but in fact it's actually the only remaining place in the entire internet that still shares information freely and without limits or fear of persecution. Mamoru, bless his weak heart, is the only person with enough gall to make a stand for the freedoms the internet is supposed to represent. Those GMD's that sometimes contain virii? Those are "bait" programs specifically left there by Officials, much like how a cop performs a sting operation in the real world.

The Secret area, where Serenade hides, is the core of the Undernet, and by extension, the ideology of the internet "personified" into a three-room private server. The Officials know of it, and have been trying to get to Serenade - and, by extension, Mamoru - ever since they found it. This is why Darkman has so many kills to his name: he's been fending off Officials, who have been desperately, obsessively trying to shut down the last safe place for torrents and illegal filesharing, for the last year. But the Undernet's virus security, coupled with the Navi and their Operators determined to protect the last safe haven on the net, have made it drat near impossible.

tl;dr Mega Man and Lan are jerks.

Lan will join/become leader of the WWW or some other villainous organization.
He and Mega Man are already the most powerful team on the Net. Soon, Lan will end up with NOTHING to do after having done everything on the Net except take it over.
 * Not necessarily villainous. Lan and Mega Man are basically Capes, so he may become a benevolent ruler protecting the net from people like WWW.

Freeze Man is Sean/Shun's navi in BN 2.
He's the last boss fought in the game prior to the Boss Rush and the Final Boss. He's also on the Kotobuki Net, which is the cyberspace counterpart of Kotobuki, where  at the time. His operator is never stated, although Freeze Man claims to have none. What makes this implausible? The only other "rogue" navi in the series is Bass, who is largely spiteful toward everyone, walks the Earth, and in brief moments where he cooperates for evil he only does so when something's in for him.

Freeze Man on the other hand has no known origin like Bass, remains in a small sphere of location, and acts entirely in the will of Gospel with no ulterior motive. His net-terrorism isn't based on his powers, either (he causes Earthquakes, as opposed to ice-storms that you would expect). Sean is also never given a navi of his own later in the series. Given that Freeze Man and Sean would have no operator/navi counterpart otherwise, and that they sort of fit together personality wise (like other operator/navi pairs), it's easy to add two plus two.
 * Shun operates Freeze Man in the Gaiden Game Battle Chip Challenge.

Mega Man's power is the forming of the battlefield.
It seems that every custom navi have their own powers in and out of battle except for Mega Man. But this is because Mega Man's ability is to form the battlefield you see, allowing him to put a set limit on how much punishment the opponent can take before he/she goes down as well as restrict movement. This is why you can even defeat enemies like Alpha, Bass, and Serenade. This is also why other navis are so much more powerful outside of battle; Mega Man also sets how much damage they can do to him. Finally, this is why Lan always shouts "Battle Routine, set! Execute!", because that's how the battlefield program is activated.
 * Does this mean Mega Man Star Force sucks at restricting enemy movement?

Roll is at least one of the sources of viruses.
This is for the games, since I only saw the anime up to the second or third season. She summons viruses to aid her in battle. It's possible that some viruses might escape. Considering she's not much of a fighter, she probably wouldn't be able to stop a lot of viruses she summoned during training.

Going by the above, Roll is a villain.
The viruses are intentional, either to slow down Mega Man and others, or to cause havoc all over the internet.

4, 5, and 6 are all non-canon to the EXE timeline.
After all, they are Post Script Seasons.
 * Nah, Star Force 2 has a easter egg where a time capsule from the Lan after EXE 6 reveals that he developed the Brotherband system. Unless you want to claim that SF is non-canonical too, but then that just leaves a branched timeline with no other branch.

Sean fell into a Plot Hole
Why else would the friggin leader of GOSPEL not be mentioned again? The same thing probably happened to Ms. Madd, Count Zap, and Yahoot.
 * Pretty sure Count Zap is mentioned in BN 6 Gregar. Colorman also kind of talks about Madd in Network Transmission. And then there was Battle Chip Challenge for all four of them...

Dr. Regal is a cyborg.
He somehow survived being a living conductor for electricity from a high-voltage cable without being fried, then jumped from the building in BN 4, and in BN 5 he is alive enough to be Big Bad. Then during the finale of BN 5 he somehow got last 10 years of his memory wiped by overload of emotion data from Soul Net (with Wily's personal help in Team Colonel version). Given how his father - Dr. Wily was extremely antisocial and thus unlikely to have a real child (except for Regal's adoptive stepbrother - Baryl, and any possible mother for Regal is never mentioned) and he was a robotics expert, it makes too much sense.
 * He's likely a full Robot.
 * A line by Mayl at the end of BN6 suggests that Iris might have been based off Dr. Wily's wife.

If a BN 7 is ever made, Splash Woman.EXE will be a badass Poseidon type
Because it would be cool to make what is unargueablly the most girly robot master after Clown Man into the most mascline Net Navi.

Dr Regal exists in the original Mega Man universe.
Self-explanatory. Dr Regal would've been born prior to split that led to the Alternate History. Logically, this means that a version of him would exist in both realities. Who knows, that version of Dr Regal may have turned out decent. That, or he became the ancestor of Dr Weil.

Dr. Hikari either removed Hub.Bat during the transition to Battle Network 2 or his hypothesis was incorrect.
. It was explained that hub.bat could cause Lan to take damage that also happens to Mega Man because now they have 100% of the same DNA. However, Mega Man is borked a couple times throughout the series yet Lan doesn't appear to be suffering any ill effects that can't be linked to something happening in real life. Maybe he either removed it so that they wouldn't "sync", or it didn't do anything adverse.
 * The first guess is correct; it's said that Hub.BAT contains 0.001% of Hub's DNA (presumably containing the information of Hub's eyes, since MegaMan and Lan's eyes have different color). But aside from that, the reason why they removed said 0.001% is to prevent both of them from synchronizing.

Lan's grandfather is alive.
How could all that info relating to Gow and the Vision Bursts stay the same after 10 years? Especially with technology rapidly advancing? Lan's grandfather is not only alive3, but put them there himself. He also sent Lan the info on Chaos Unison.