Charmed/WMG

Billie was born from the Nexus being destroyed.
Billie is a reality warper and has all sorts of powers despite her young age. She also appeared out of nowhere at the beginning of the eighth season. She could have been born from the Nexus energies and used Prue as a basis to get close to the sisters. She might have also created a connection with Paige to become her charge. Billie then created a past for herself so that she would connect to humanity easier. After being exposed to the sisters and feeling angry at their selfish ways, she subconsciously created Christy and even manipulated demons to think that they had held her captive for years.
 * This actually makes tons of sense to me, since they was absolutely no in-verse reason why the so-called Ultimate Power went unmentioned by anyone before they showed up (because they didn't exist before they showed up). Thanks for the new Fanon.
 * Unfortunately, there's also the part where this reeks of Ron the Death Eater, especially since the Where Are They Now Epilogue and the revival comics depict her as merely a capable witch and a friend to the Charmed Ones, with ever her "fuck reality" power never really emphasized again.

Charmed takes place in the "Ultimate" style universe of Smallville
This theory was somewhat confirmed by one plot point of either a season 6 or 7 episode which had Wonder Womans girdle. Actually Hippolyta's girdle which was found by Billie in a chest of previously unknown magical artifacts and in a short bit of Exposition Hippolyta's youngest daughter (aka Donna Troy/Wonder Girl in the comics) tried to wear the girdle but was destroyed by its beyond awesome level of magic. Billie tries on the girdle herself and nearly dies herself.

To boot the costume generated by the Girdle as Billie puts it on looks suspiciously similar to a image from a 2005 or 6 Wizard Magazine issue which has a Alternate Universe Wonder Girl costume which according to the related article came from a "Ultimate" DC Comics universe which was an offshoot of TV series Smallville.

And as a final nail to the foundation both Smallville and Charmed were CW/WB network series which while it never happened a Crossover could have been a possibility although this would have been Hilarious in Hindsight as Clark would have most likely become the designated Damsel in Distress due to his physical weakness to magic in which the Halliwell sisters would have to bail him out of constantly.

The Triad has Cole's father's soul because they wanted to stop him from being reborn.
Reincarnation is mentioned frequently in the series. Phoebe also says that Cole's father had done a lot of good things when he was alive. The Triad (or the Source, or some other demon) could have intercepted his soul after he died to prevent him from either becoming a Whitelighter or being reborn and doing more good in the world. Cole could have made his deal with the Triad so he could release his father's soul.

Charmed is the imaginary adventures of three girls playing with their Barbie dolls.
This is why so many of the Charmed Ones's crushes and love interests are lantern-jawed white guys - they're Ken dolls.

Prue was destined to die from the start by the Elders
The Angel of Death basically tells her she's destined to die in S3, which seems odd in retrospect (why would a Charmed One be destined to die from The Powers That Be?) but less so if you consider the following: Piper and Leo already showed in Styx Feet Under, S8, that cheating death is impossible; if he's really out for you, its only a matter of time. Prue had a really sharp concentration of near death expeiences in her tenure, nearly dying in The Power of Two but before being given CPR by andy, to the S2 finale (where she's stabbed by the dragon and then rezzed, something which this troper imagines would also further p*ss Death off, further giving him cause to go after her) to the S3 finale (where Leo first heals her) and then finally in S3 again where Death finally catches her. Just as in S8, Prue may have been slated for death so that the bereavement would act as a motivator for the sisters to kill the source, which it did, as they planned for Leo.
 * It wasn't the Elders that destined Leo to die, though. This kind of thing is above their heads. We're talking Angels of Destiny level stuff right here, we've seen in canon through Leo's case that this is their department. Why else is it that Grams can visit the sisters as a ghost after a year and a half, but even after all the years that go by, they still never get to see or even hear from Prue? The Elders and the Avatars have been defied by the sisters before for trying to play God with their personal lives, so there's no way either of those two groups could be behind this.
 * Oh yeah, trufax...so it was the Angels of Destiny then?
 * Bingo.

The Smexy Genie from the S2 finale was at least partially responsible for Prue's final death in S3
Think about it: Genie wishes are notorious for being complete monkey paws (even when the genie isn't trying to be a jerk) and this is demonstrated throughout the episode multiple times. Hence wouldn't it be logical, even natural, for her resurrection wish to also backfire, say, by only granting Prue temporary resurrection before being killed off again in, say, the next season finale? This would explain why she couldn't be saved from Shax even by time travel and why Death told her she was destined to die then.

The Sisters Don't Do Ritual Spellcasting Because They Don't Need To
The in-verse reason the sisters gradually become less dependent on ritual (like we saw for most of the Burge era) is because - being the most powerful witches ever to exist - they are strongly magical enough not to need to build up ritual energy to cast spells. Likewise, as the series progresses they become stronger and stronger witches and so by the end all they need is a quick rhyme and they're good to go! Compared to the first episode for example, "Something Wicca This Way Comes", which was relatively very ritual heavy (in fact, despite being new witches, they probably didn't even need to do as much as they did & were most likely being - understandably - overly cautious). Other normal, magical witches would probably have to go through a relatively complicated series of processes to achieve some of the feats the sisters have with just some hocus pocus, like casting an illusion on every man on the planet in "Styx Feet Under".


 * So basically, the premise of Young Wizards.

The Elders and/or Angel of Destiny killed Grams
Pretty self-explanatory - we saw in Pre-witched that she was about to stop the sisters from inheriting their powers before she just so happened to have a heart attack. Coincidence? I think not.

The Elders can only bring someone back from the dead (as whitelighters) once, or else
Hey, it would explain why Natalie had to die (other than angst, obviously).
 * What about Sam?

Prue created the Cleaners.
The Cleaners have not done anything until they first showed up and they have the power to alter memories. Prue could have been worried that exposure of magic is much easier now with all the technology and so she got the Elders and the Demons to create the Cleaners. But, to give the Cleaners more credit, they made it so that they were at least active for eternity when in reality, they were around for only a few years.
 * Alright, going by this combined with the Angels of Destiny theory surrounded her death…just what exactly is Prue now? I mean, she can't be God; the season 8 Angel of Destiny has hinted at God running/being the Grand Design itself.
 * Well Prue did become an Empath for episode, and combined with the Power of Three, she could have possibly had an imprint of the entire world left in her spirit and with this, her spirit could have had enough time to contemplate what her sisters really needed. She possibly even is the reason Cole learned to want Phoebe to just be happy.

Andy became a whitelighter.
Leo's first wife told Piper that he dreamt about Leo after his death. Kyle also said goodbye to Paige. The scene where Andy says goodbye to Prue is eerily similar to the situation described by Leo's first wife.

Higher forces were responsible for Piper and Phoebe's career successes.
Because the forces of good wanted to make sure they had enough money to keep the house.