American Dragon Jake Long/WMG

Jake's grandmother was a member of the Huntsclan
In the first episode, when Jake notes how hot Huntsgirl is, Lao Shi warns "Grandpa has been there." We haven't heard anything about Jake's grandmother, so it's plausible that Grampa keeps silent about her - and discourages Jake's romance with Rose - because things between Grandpa and his Huntsclan girl eventually turned out very, very badly.
 * I believe you are sort of correct. But Disney higher ups said no to that.
 * AFAIK, Disney said "No" to Chang being Jake's grandmother. Producers Eddie Guzelian and Matt Negrete said that the issue of Jake's grandmother would have been dealt with in the third season, if it had come to pass. At one time, there was a plan to reveal that Jake's grandmother was killed, and so Jake would seek revenge, but was dropped early on. Still, it doesn't rule out the theory.

Lao Shi is a barefooter.
In Season One, we mostly see him with sandals. A few times we see him barefoot indoors. But in Season Two, he seems to go barefoot outdoors as well. That's another reason why he wears a robe, so no one can see he doesn't wears shoes. His foot fungus seen in "Old School Training" is either the result of being barefoot or the reason why he goes barefoot.

The Am. Dragon, and every other dragon person, is actualy a mutant.
They exist on the X-Men realm and they have controlled there mutation to the point where they can ensure that it is passed on.

Right after the series finale, the Magical World was exposed by an Alien Invasion.
Characters from both American Dragon: Jake Long and Kim Possible made an appearance in Lilo and Stitch: The Series, so we can consider them part of the same continuity... And right after Jake's travel at Hong Kong, Kim Possible had to deal with the Lowardian assault on Earth. If the dragons didn't come out for that...

The Huntsman was half-blind but didn't want to admit it.
During the second season he never noticed that the dragon Rose supposedly slayed at the Academy was in fact the American Dragon until #88 and #89 didn't flat-out told him that, and was later convinced it wasn't when Rose brought Jake's moulted skin, without noticing any difference. Also, he somehow failed to notice that the American Dragon was identical to the Dragon that kicked him in a pit with a giant crab monster years earlier, triggering his deep hatred for dragons and deepening his then-highly pitched voice (thanks to a bit of Time Travel). Either he's an idiot, or his sight is so low he's pratically half-blind, and he will never wear glasses.

The Huntsclan were originally allies of the Dragons.
The first Huntsclan members (who probably weren't called the Huntsclan, but whatever) were human warriors that aided Dragons against evil magical creatures before The Masquerade set in. They were gifted with power from the Dragon they partnered with in the form of a dragon-shaped birthmark that passed down through their bloodline and made them stronger when fighting with their chosen dragon (like Pactios in Mahou Sensei Negima). As the Magical World faded into hiding the humans felt abandoned by their partners and gradually turned into the Huntsclan; they still drew on the power of dragons through the trophies they took from them like the skull helmets all full Huntsclan members wear, though this was a weaker and perverted use of the relationship. They kept track of the bloodlines so they could steal infants like Rose when they manifested the mark, now sincerely believing it was their destiny to kill dragons instead of being partners with them. Rose's relationship with Jake reopened the original partnership and explains why she can handle multiple Huntsclan members and fight the Dark Dragon to a stand-still.

The Huntsman really IS Rose's uncle.
Not only was one of Rose's parents is related to him, s/he was also once a Huntsperson. My guess points to Rose's mother. She and the Huntsman were very close, and their family were members of the Huntsclan and a very high-ranking and influential class. But then Rose's mother began to think their ways is wrong. The Huntsman was shocked to hear that and tells her never think that again. She herself fell in love with a Dragon she was chasing. The two have a secret relationship like Jake and Rose. But the Huntsclan soon finds out and ambush him. Rose's mother was devastated to find her lover's dragon head mounted. The Huntsman was furious of his sister's transgression which shamed their family within the Huntsclan ranks. Realizing there's nothing left for her in the clan, she decides to defect (a move that's considered treason and punishable by death), changed her name and began a new life. She eventually meets her future husband who's in the dark of her past. After many years, the Hunstclan was able to find her upon her pregnancy, which the Huntsman handled personally by taking Rose to raise her as a Huntsgirl to make up for her mother's shaming of the family. As far as the Huntsclan is concern, Rose's mother is dead to them. She'll likely approve of Rose's relationship with Jake because it reminds her of something she once had that could have grown.
 * Alternatively, both parents were slayers who left the Huntsclan to start a family and had to leave the Huntsclan because slayers who start families are believed to become soft and the only reason it's not completely discouraged is because someone needs to make the next generation. Rose's parents just pretended to think Jake was delusional so they'd rid of him without Jake suspecting.

Spud's family are actually wizards.
He was shown having magical potential being able to use Panderis' wand, his grandfather knowing how to seal away the genie in Taranushis Chalice and also telling him stories about the mermaid city

Rose never had a sister.
It only appears that she did because You Already Changed the Past. The "twin sister" is actually the alternate Rose created by Jake's wish.

Rose's sister became a slayer in the new timeline.
The skulls granted Jake's wish by making the Huntsman take her instead of Rose.

There's no new timeline, only memories of it. Due to this, Rose's twin is still around the world searching for her lost sister, and their parents have both sets of memories
Jake and co. remembers only the timeline of Rose as a member of the Huntsclan (and Jake kept physical proof of it, and Rose somehow kept her skills as member of the Huntsclan and could recover her memories of the old timeline. This makes little sense and create a time paradox (including how or why Jake made his wish), unless the Skulls didn't have enough power to actually change the timeline and did the best approximation they could: change memories and various records to make it look that way. Jake and co. kept their memories because, being present when Jake made his wish, their memories were too strong to be changed. In the meantime, Rose's twin had ran from home to try and find the twin sister her parents always complained of having lost and to which she was unfavorably compared (like "If Rose was still here she'd act better than this"), if only to show them what her sister actually was. When Jake made his wish, the Skulls tried to change her memories, but she wondering 'why the hell am I here?!' prevented it, and she's still searching for her. Finally Rose's parents got both sets of memories due the other daughter's escape to search for Rose, but fakes remembering only the set where Rose was not kidnapped due to fear of losing their daughter again, and react harshly at Jake because he's there to take her back to the old life of danger. Sadly for them, Rose recovered her memories of the Huntsclan by seeing the picture...