The Middleman/WMG

Tyler's job will bring him into contact with the Middleorganization, one way or another.
Well, it's important to the plot somehow. There are two opposing possibilities here:
 * 1) Manservant Neville is a Lex-Luthor-type supervillain. Tyler will not immediately figure this out; but eventually, Fatboy Indutries will go up against the Middleman, and Tyler will be quite surprised to find out what Wendy does at work all day.
 * 2) Fatboy Industries is O2STK. After all, Tyler was almost recruited for Wendy's job; presumably, the Middleman's bosses are looking for the same qualities. They'd certainly have the technical expertise to repair Ida and provide the various Middlegadgets. Since O2STK (or, as they called it then, WTHWWF) has been operating at least since 1969, someone else was probably running it before Manservant Neville.
 * The battery of tests they gave Tyler, and the fact that almost anybody played by Mark Sheppard is evil or slimy, suggests that Fatboy Industries is the opposite number of O2STK - a Murder, Inc. joint - and Manservent Neville is the opposite of the Middleman. Because that would be awesome.
 * According to Word of God, [spoilers for the graphic novel].
 * Now that the unproduced final episode has had a table read and come out in graphic novel form, we know that
 * Note that the Mirror Universe Manservant Neville turns out relatively benign, which is an argument in favor of door #1.
 * Possible evidence of O2STK being connected to Fatboy: The instruction booklets for the Concussive Stun Field Generator and the Truth Bomb contain an image of Fatboy's mascot. See a screencap here.

The Middleman is Wendy's father
Somebody had to be. Aside from her constantly mentioning her missing father - a Chekhov's Gun waiting to fire - there is evidence for this one:
 * He knew about her lighter. (There are other ways he could have known, but...)
 * When under the influence of the Truth-Sphere and asked what his real name is, he says, "My name is... the same as my father's". Admittedly, we don't know if Wendy's dad is named after her grandfather, but it still seems interesting.
 * The tarot card girl tells Wendy, "You spend too much time with your father." This is patently false unless her father is the Middleman, whom she likely is spending too much time with (he interrupts her dates and bonding time with Lacey, among other things).
 * When the watch picks up Wendy and Tyler exchanging pleasantries, he says "Wendy's like a sister to me". Obviously just a turn of phrase, but it could be foreshadowing.
 * In general, the Middleman's attitude toward Wendy is not unlike the way a father-figure would act, as Wendy has said. Though, he's more of a male Cool Big Sis, if that makes any sense.

There are unresolved questions (he looks a bit too young, but maybe he has an anti-aging serum or something), but it wouldn't be too surprising.
 * Alternatively, the Middleman is Wendy's brother. This would explain all but the tarot, but she gave inaccurate readings anyway. The Middleman may or may not be aware of this. (This would make the Middleman's real name Peter Watson.)

Wendy's father was a Middleman.
Similar to the above. Wendy's father was a Middleman, perhaps the mentor to the current Middleman. This might explain why he disappeared -- he was killed on the job, cryogenically frozen, or sent on a long-term mission.
 * (Graphic novel:)

Wendy's father is Sensei Ping.
You know, just to cover all the bases.
 * Wendy is incredibly successful in martial-arts training. Maybe it's genetic, or maybe she was being surreptitiously trained as a child.
 * Lacey talks about how Wendy used to paint "airplanes, Asian guys, and Asian guys in airplanes," which strongly suggests that Wendy's father is Asian. Who's the only major Asian character on the show? Oh, right.
 * Wendy doesn't see Sensei Ping's face much in "The Sino-Mexican Revelation." Maybe he keeps it covered somehow in her unseen training session(s); it's almost plausible that she might not recognize him (at least, relative to the probability of her not recognizing the Middleman...).

Wendy's father is Ida.
What? No takers on this theory? Okay, fine.
 * Taken. Wendy's father was killed working for the Middleagency. The current Middleman (his apprentice) dragged him into a cold storage tank too late to save his body but early enough to upload his mind. His mind was affected by the original Ida's mind. The original Ida was a defective fembot programmed to be attracted to Middlemen and downright murderous toward human females who could affect her mission. The "frumpy" look was adopted to suppress possible issues. In the Alt World, Wendy's father died before the current Alt Middleman could rescue him, so Ida kept the fembot look.

Wendy's father is Noser/Lacey.
He was re-incarnated and advanced through school to the illegally sublet studio apartment stage of life more quickly thanks to his having been through school before, and possibly being a Middleman. He set out to find Wendy and help her through life, either as a morally steadfast roommate who tended towards Obfuscating Stupidity (well, Obfuscating Ditziness, anyway) or a guitar-playing, Cryptic Conversation-having, Zen Survivor of a ventriloquist. Of course, Younger Than They Look applies (as well as the body-switcher version of Older Than They Look). If Lacey, either the pitcher-shapes-the-water effect is what gave him the crush on the current Middleman as in the Ida guess, Wendy's father was bisexual or had If It's You It's Okay situation for either her mother or the current Middleman, or they both knew and it was a way to transmit coded messages without Wendy realizing.

Roxy and the Middleman were romantically involved once upon a time.
He just takes her breaking of their deal so personally and is so quick to forgive after a little bit of flirting.
 * Granted, Roxy is a succubus, and flirting her way out of trouble is doubtless second nature to her; but one would assume MM is made of stronger stuff than that.
 * Roxy is a succubus. It's unlikely that she wouldn't at least try to get our boy out of those unflattering pants.
 * Read this: http://brista.livejournal.com/4538.html

Planetary is the O2STK
This one's a bit... involved, but hey.

The Planetary organization is TV Tropes Made of Win Archive, but their comic has slipped off the regular shipping list. Since they launched, the Wildstorm Universe went through a bit of a revamp; we have no guarantee that they made the cut.

So, imagine that Planetary got pushed out and got pushed into a new universe, the Middle-World (we can't call it Middle-Earth, can we?). They set up shop; the rest, as they say, is history.
 * The Wildstorm revamp was in 2007, and Middleman started in 2008. So there's time.

The show is set in the same universe as The Lord of the Rings
Tolkien turned out to be wrong about ALL the magic having left the world. O2STK is the Valar, determined to keep their involvement in the world today to a minimum. Plus, this way, it can take place on Middle-Earth.

Middlemen (in the show) are grown, not trained.
Wendy is only being trained because her father was the first non-sterile Middleman and they need to test her as the Super Prototype for Middlewomen, who would be cloned from her.

O2STK is a division of U.N.I.T
Makes sense. Why else would they be governed by the Treaty of Perpugilliam or have a Zygon-Rated Quarantine Facility"
 * A throw away line in this FanFic makes for a nice connection.