Billy Kaplan's original superhero name, "The Asgardian," makes sense in light of Norse Mythology, where the type of magic practiced by Odin, known as Seiðr, was infamous for its connotations with homosexuality and feminity. Loki once taunted Odin for practicing it, essentially calling him a "girly-man." As a Norse mythology geek, Billy was most likely aware of this and therefore used his nickname as a way to take pride in his sexual orientation!
Related to this, the fact that Loki apparently has no problem with Billy and Teddy being gay seems odd until you remember that, as a magic-user, he was likely assumed to be/accused of being gay himself, and doesn't see it as a bad thing.
Plus He once turned into a female horse and had sex with a male horse giving birth to Sleipnir
And now Loki has pointed out that he grew up in a time where sexuality wasn't split up the way it is and makes a pass at Prodigy.
Why would a pagan god subscribe to moral norms rooted in the Abrahamic religions? This has been toyed with in The Incredible Hercules where writers have at least started to acknowledge that in Ancient Greece people (and gods) were not exclusively heterosexual.
Also consider the couple of Billy and Teddy: one is a strong, handsome, good-natured blond who tends to depend on his physical strength in fights while the other is a comparably-weaker, snarky, dark-haired magic user. Loki's plan to plant seeds of mistrust between the two to break them up may be caused by him working out a few issues between himself and Thor.
Prodigy's status as an outsider, unaccounted for in Loki's plans, means that the former X-Man is now a literal X-Factor.
America's sexual identity is an inverse of the typical cis-gendered heterosexual girl. She comes from a universe where it seems being a lesbian is not only accepted, but hinted at being the norm judging from her mothers and the other couple who brought the news of her mothers' deaths. She also briefly experimented with the Ultimate Nullifier before ultimately accepting that she was lesbian.
Billy's depression and some of his outright erratic behavior during The Children's Crusade might have a simple explanation when you remember everything he went through during the Civil War, from being captured and forced to watch as his boyfriend got vivisected by a mad scientist to being held as a POW in the Negative Zone. He's most likely suffering from PTSD!
Teddy's proportions tend to vary from issue to issue. At times he's barely an inch or so taller than Billy with the same body mass, at others he towers over his teammates and become much wider and bulkier. While you could blame shifts in artistic style from different artists, there's also an in-canon explanation: Teddy's a shapeshifter. Of course he can change his proportions depending on his mood or the situation at hand!
Confirmed in his backstory. Teddy originally used his powers to become more buff so as to fit in with the jocks at school, even though his super strength works just fine when he is human-sized rather than hulked out. Also, the Super-Skrull used a device on him to force him into his true form, which as it turns out is exactly the same as his regular teenage appearance. Every other appearance he assumes is a function of shapeshifting and may reflect his current frame of mind.
Issue 6 of the 2013 run confirms that Tommy has sped up time perception like Pietro. It's stated that in juvie he was experimented on. Imagine how that would be for someone who feels five minutes as a week.
This same thought applies to whatever it is that Fake Patriot has done to him, or wherever he's been taken.
During the team's lovely trip through The Multiverse, they find horrible alternate realities, most of which are post-apocalyptic hell-holes. As Kate stated, it's entirely possible that Earth-616 is the best of all possible worlds. That's right, a world where America went through several devastating civil wars, where mutants are regularly discriminated against and nearly wiped out every other decade, where people constantly have their loved ones die (and maybe come back somewhat sane and functional} is the best of all possible worlds!