Note! This entry will contain major spoilers for those not yet invested in the show and will discuss things which I think may have a high probability of happening in the remainder of the series.
So we know that Stan's big secret, that he was building the machine whose blueprints were outlined in the author's journals, in order to open a portal that his brother (who is also the author) apparently fell into 30 years ago in an attempt to retrieve him. The series has done a masterful job for the most part of keeping the big reveal only hinted at, never drawing outright attention to the clues while still making the same clues present.
The trailer for the next episode has aired (A Tale of Two Stans) and looking through the rapid-fire images, a picture is starting to develop. It would appear that the two Stan Pines (Stanley and Stanford) got along really well when they were very young. They were the "Original" mystery twins, getting into adventures and generally looking out for each other, but at some point, their paths diverted from one another. Stanley focused hard on his education and into his work in academia while Stanford goofed off and slid into get-rich quick schemes that, over time, gets him banned in just about every state in the country. They part with their relationship severely strained. Stanford is at this point, the "Black Sheep" of the family. Personae non-grata, as the saying goes. To the rest of his family he's such a disgrace that he's never even brought up to his own Grand-niece and nephew that he even exists. Fast-forward in time, and it turns out that Stanford has been banned from just about every state there is to be banned from (hence all the fake ID's), except the one his brother is residing in: Oregon. He goes and pleads his situation to his brother, and Stanley reluctantly takes him in. For awhile it may even appear that their relationship is mending, with Stanford even assisting his brother and McGucket on the first incarnation of the portal device, but eventually Stanford gets tempted by the potential for the secrets in his brother's Journal to make him a quick buck, quickly sending their relationship to an all-new low. He may even through his own selfish action or inaction, cause the accident which endangers McGucket (as seen happening in a flash in the trailer) and perhaps sends his brother through the portal.
McGucket, so traumatized by these events (and perhaps having seen things that would drive a man insane because of the accident), takes the journals, adds the earth-shattering warning against using the device himself, and hides the journals to further prevent anyone from reconstructing the device. He then invents the device that will erase his memory and becomes the McGucket we know today, as shown in "Society of the Blind Eye". Stanford, racked with guilt at being directly responsible for these tragedies, and despite the fact that he himself is no genius, tries to and finds at least Journal #1 in an attempt to do just that: reconstruct the device in an attempt to retrieve his lost brother and atone for his own sins. He stages his own death and adopts the role of his brother (whose name he may have swapped as well and the car with "Stanley" on it really was his all along,- not sure how they'll handle this detail), taking over ownership of the shack, and turning it into the tourist trap we were introduced to it as at the beginning of the show. Stan uses his past experience in shady dealings to what he sees are good ends: Every bit of money we think he's hording greedily is actually being put into reconstructing the device as per the instructions left in the journal and his own recollection.
Enter Mabel and Dipper. Their parents believe they're sending the kids to stay with the other, reputable brother, not realizing the events that have transpired, and so the kids believe the same. Dipper finds Journal #3 and the rest plays out as seen already to up to the most recent episode ("Not What He Seems"). Dipper in the preview asks, naturally, why Stan would hide this from them, but if what I suspect is true, then it's completely understandable why Stan would be so reluctant to share all this. For the first time in probably forever, he's experiencing the life he denied himself by being the black sheep. He gets to bond with family, something he at this point desperately misses. Revealing the secret is to reveal the very darkest part of his own past, one that at this point in his life he is deeply, deeply ashamed of. In his mind revealing it would effectively end this wonderful time he's been able to share with these kids.
Where the show goes from here? It's been heavily implied that Bill Cypher has plans of his own involving the activation of the device. He may have been part of the visions McGucket saw in his accident, which is why in McGucket's memory tube it appears that he's making the "Bill" symbol with his fingers and eye. Indeed, the portal may inadvertently have caused the conditions necessary to bring Bill out of the Dreamscape and into reality, where his chaos is no longer limited by having to make the devil's deals with ordinary mortals in order to achieve his own ends. This, I think, will form the core conflict for the remainder of the series until it ends (I believe it's been said that this series was written with a particular end in mind, and it seems we are rapidly approaching it).
The events will bring all the major characters as well as several of the minor ones who we've come to know better especially in season two (such as Robbie, Pacifica, etc) into this conflict and in the end I believe it will be Grunkle Stan himself who will end up having to make the ultimate sacrifice, finally atoning for his mistakes and restoring his reputation not only in his brother's eyes, but of those in the hearts of Mabel and Dipper as well. The writers have for a long time had this peculiar habit of introducing various avatars of "Stan" which end up routinely getting obliterated: (Wax-figure Stan, Scrambled-egg Stan, Piniata Stan, Puppet Stan, Hot-air Balloon Stan), not to mention that at the end of "A Land Before Swine", the writers literally have Stan fall into an open, empty casket. Knowing what we know how the writers are so adept at weaving small things into the story to hint at future developments, I think this one is highly likely.
In the end, the theme which ties everything together (and what I think may really truly push this show into something that will go on to be remembered fondly the same way Avatar the Last Airbender did) will be that of Dipper and Mabel coming into a new sense of maturity in themselves, and their own sibling relationship having seen parts of themselves in the elder Pines twin's relationship, struggles, sacrifice and forgiveness. This is the summer when the twins Grew Up.
Lots of foreshadowing in the series hinting at that as well, signaling the end of one phase and the beginning of the next. Brings a whole new meaning to the phrase "Everything will Change", doesn't it? I don't think by the end it will only be a phrase used to describe the physical world in the wake of the portal's activation, but in the personal lives of all the main characters. If true, that'll be some heady stuff for a cartoon modeled around the humor of shows like The Simpsons and Futurama, atmosphere and mystery reminiscent of the Goonies, X-Files, etc.
Perhaps just as important a message the twins may get from it is that no matter what happens from this point forward, no matter how much one or the other may screw up, or even break trust, never give up hope for them. That's another theme the show has been hitting on repeatedly in numerous episodes, but this would be the example to end all examples. A completely self-centered con artist who ends up giving everything up, even his life, for the sake of family.
Anyway, just wanted to get this on record before we get the actual story laid out and to have something to compare my thoughts now and my thoughts afterward.