Jay is Manny's biological father.
Manny looks exactly how you'd expect the son of Jay and Gloria to look, even if he's supposed to be adopted. So he isn't. Gloria met Jay 11 years ago when he looked much more attractive. They had a relationship, Manny was born, and when Gloria broke up with Javier she went back to Jay.
- The only flaw in your reasoning is that 11 years ago, Jay would have looked like Al Bundy.
- I don't think Jay would look as bad as Al Bundy. Al Bundy at Jay's age probably looks a lot worse than Jay does.
- When Cameron morphs a picture of Gloria with Mitchell, the result looks a lot like Manny.
Jay is a mob boss.
We don't know what he does, only that he's rich, so...
- Cleared up a little in a season two episode where we get to see some of what he does. It's still mostly ambiguous though.
- Jossed in the Season 3 episode "Hit and Run", where we see that Jay manufactures closets. In the same episode, Manny is doing a school report on The Mafia, and neither he nor Jay act like Jay has any special knowledge of the subject.
Phil is not Haley's father
Would explain why Haley seems to be the odd one out, physically.
- She has a lot of his other traits though.
Luke will grow up to be a Rorschach
He already doesn't trust the police, and we've seen his semi-violent nature via the squirt pistol. It's only a matter of time.
- Only to be foiled time and time again by the Boxmaster.
- Considering his entire Godfather-esque montage recently, Luke may grow up to a vigilante for a criminal organization.
Manny is gay
It wouldn't be too far off for this to be revealed if the show runs long enough:
- Although this show isn't crazy about gay stereotypes, some do appear: Mitchell is a fan of musical theatre, Cameron is flamboyant and a fan of various pop icons like Cher and Madonna.
- Manny's "stereotype" is his interest in fashion, or at least in looking sophisticated in suits and other clothes. Remember the puffy shirt?
- When Jay tries to tell Manny off for something, he most frequently compares him to Mitchell (Manny's poncho and Mitchell's "jaunty scarf")
- It's probably more likely that Jay's looking for someone to relate to and share his interests with. Note how he gets along in a much more casual way with Cam, in no small part due to Cam being a football fan. Compare this to Phil who's a man-child, and Claire and Mitchell who has very different interests.
- Although Manny is teased for different reasons (being Colombian, too mature, overweight) when he needs advice about being "different" he most often gets it from Mitchell or Cameron.
- I always thought Manny's sophistication and interest in fashion were a way to portray him as a very young, modern dandy.
- Jossed by "Best Men". Manny seems quite interested in the female form in a sexual way.
- Explained in other episodes; in "Yard Sale" Mitchell and Cam both point out to Alex that they dated women before they came to terms with their sexuality. In fact, Manny's exaggerated interest in the female form could be explained as a coping mechanism, overcompensating for something he thinks he should feel but doesn't.
- That said, at Manny's age in the first few seasons, he's too young to properly have sexual urges either way.
Haley got abducted by aliens and is replaced by an alien replicate
Would explain the massive Flanderization
she experienced somewhere around the middle of Season 2.
Jay and Gloria's baby will be a girl.
- Jay made it a point to mention that he'd prefer a boy and knows how to raise them, so he and Gloria will end up with a daughter. Especially since Gloria already has a boy and wants a girl.
Haley's arrest and expulsion from college was meant to have happened offscreen
- The sequence of episodes for the second quarter of the fourth season seems a little off kilter, as their production numbers reflect. *"Arrested" dealt with Haley getting arrested for underage drinking, assaulting a police officer and resisting arrest after she tried to flee a party during a police raid by jumping out the window ... and landing on a cop. Despite a very sincere and mature speech to the college's disciplinary committee, she was expelled (all of five weeks after starting school) with the proviso that she could reapply the next year.
- The end of that episode seemed to set up her return to the Dunphy house and the show's regular diegesis. Yet in the very next episode, "Mistery Date", she's not seen at all, and Claire makes a passing reference to getting email from her as if she's still at school.
- At the beginning of the next episode, "When A Tree Falls", she and her parents are shown sitting on the couch talking to the Confession Cam, recounting the events of "Arrested". This is a little odd because usually things we've already seen, even in a previous episode, are not reiterated in this fashion.
- After Thanksgiving, the last of the fall episodes, "A Diamond in the Rough", aired. This concerned Cam and Claire turning a vacant lot into a field where Luke and Manny's baseball team could play its championship game. This episode aired in early December, closer to Christmas than the last game of the World Series, a rather odd time in the U.S. TV season to be running a baseball-themed episode (and oblivious to the fact that most youth baseball leagues end their seasons before the school year even begins).
- Is it possible that "Arrested" was written quickly and shoehorned into the schedule, bumping "Diamond in the Rough" to a later, less plausible date after the writers (or somebody) decided Haley's arrest and expulsion was a story better shown than merely alluded to?
The show started with Lily coming into the family (birth), and will end in Jay's Death.
Haley and Dylan will get married, and get their own portrait sequence in the opening credits
Haley and Dylan will get married once Haley hits her mid-twenties circa Season 7 or 8 (if the series lasts that long).
Simply because the producers seem to love Dylan so much
! Every time they try to write him out as the necessary and fondly-remembered First Love
but ultimately the wrong guy for Haley, or introduce another viable-seeming love interest for her, he pops up again by the end of the season and steals the show. According to this pattern, eventually they'll marry them off and promote Reid Ewing to main cast. While they've been deliberately avoiding marrying Haley off young (as when she rejects his proposal in the Season 3 opener), she'll be 22-23 and (hopefully) graduating college by the end of Season 8, which seems like a realistic age to marry one's High School Sweetheart.