So: in the ongoing investigation of space opera, I've looked at cliches, I've tried to come up with a rough definitional rule of thumb ... but I've avoided what's possibly the largest elephant in the room, namely, plot structures.
A key aspect of space opera is that it's about epochal events and larger-than-life characters. Most genres can be written to work in a variety of modes; for example, consider the difference in the level of melodrama in spy thrillers betwee James Bond and Graham Greene's The Human Factor. Similarly, high fantasy can be quietly introspective and pastoral, or focus on the clash of kings and dark lords, and horror can run the scale/focus gamut from The Yellow Wallpaper to The Stand.
But space opera is different: it's almost impossible to conceive of a space opera with a plot that revolves around the eqivalent of a middle-aged English professor's mid-life crisis as he carries on a furtive affair with one of his female students under the nose of his long-suffering wife (the somewhat cruel stereotype of the MFA-approved Great American Novel). I mean, you could do it, but your professor would have had to have invented a new type of FTL drive that threatens to revolutionize interstellar travel, the student is a spy from a cartel of space traders and is trying to get the blueprints out of him before she stabs him in the kidneys (because: lecherous middle-aged prof, ew), and his wife—the professor of political science at Galactic U—is actually a retired assassin (and just wait 'til she finds out about the student). Into the middle of this quiet literary novel of academic infidelity and domestic lies, we then add an evil religious cult of alien space bat worshipers who want to steal the new space drive to equip their battle fleet when they sweep in from the Orion Arm to bring fire, the blaster, and the holy spacebat inquisition to the Federation, and when they kidnap the professor his wife and his grad student have to work out their differences to get him back before he cracks under (well-deserved) torture and gives the fanatics the ultimate weapon ...
(Huh. Actually, that'd make a cracking space opera; just not one of mine. Anyone want to borrow it?)
I stand by my point: you can't write space opera without ramping up the stakes to melodramatic levels. (Well, maybe you could if you were Iain M. Banks, but he was special that way.) The need for romanticist drama is one of the pillars of the sub-genre. And one of the recurring core tropes of the genre, which is so fundamental you can hardly call it a cliche (any more than boy-meets-girl/boy-loses-girl/boy-gets-girl is a "cliche" in genre romance) is the Campbellian Hero's Journey.
If you are reading this blog you are familiar with the Hero's Journey monomyth because it's ubiquitous in our mythology and entertainment. Campbell derived it from studies of myths in many cultures, publishing his exposition The Hero with a Thousand Faces in 1949: his theory was that major myths from various world cultures can be traced back thousands of years and share a common cyclic template (with roughly 17 stages). Since then, it's been used repeatedly by entertainers as a construction template; for example, Christopher Vogler more or less codified it as a recipe while working for Disney studios. The plot of the original Star Wars trilogy was an explicit appropriation of the HJ cycle by to George Lucas (to be fair, before Vogler's codification); it's no accident that Darth Vader is Luke Skywalker's father (Vader is Dutch for "Father") or that the fight between Skywalker and Vader in The Empire Strikes back is one that Skywalker loses—but survives to re-fight more successfully later. A key feature of the monomyth is that the hero leaves home on a quest, faces challenges, confronts and is struck down by his father/the darkness, then rises again, atones/achieves enlightenment/excellence, and triumphs in a final struggle that represents maturation.
Campbell's work isn't uncritically or universally accepted, to say the least, and there are variants on it: for example, Valerie Frenkel critiched him for focussing exclusively on the male variant of the Hero's Journey. It turns out that there are plenty of recurring myths where a version of the monomyth applies to women, with similar but distinctively different recurring stages focussing on the heroine's progress from girl to mother. Rather than fighting to defeat/overturn the parent, the heroine's struggle is to become the parent: rather than returning to the original home but as master (the male branch of the monomyth) the female version has her joining a new household as its mistress and new mother or goddess/priestess.
Yes, this is all horribly gender-stereotyped. But I'll take a stab in the dark at diagnosing its origin: the stages in the monomyth echo the mammalian K-selective reproductive cycle—on hitting puberty the young adult leaves the nest/parents, goes looking for a mate, meets and overcomes obstacles (competitors and predators), finds a mate, forms a new mated pair. In the case of humans or other primates there may also be issues about troupe/pack hierarchy to be resolved. Yes, there are problems with this: it doesn't map onto social structures once established settlements and agriculture become the norm and the young adults are expected to stay home and plough the fields. But the monomyth remains deeply appealing because the mythic framework it builds on has very deep roots that go all the way down to primate reproductive biology.
The monomyth doesn't have to be melodramatic: you can, at a pinch, apply it to that stereotypical MFA lit-fic novel of lecherous middle-aged academics without too much trouble. (The journey is one of internal psychological discovery, the threats are the protagonist's inner demons, the allies are the psychiatrist, the crisis/conflict is one of understanding ...) But as often as not, it's a structure for heroism: melodrama acts as a spice, raising the stakes and giving us a reason to pay attention to the protagonists, for their deeds are significant and implicitly may affect us (or the proxy the author has provided for our viewpoint).
So: Space Opera. Take the monomyth as a framework for how the action unfolds, and mix it up with melodrama. Then add space ships, ray guns, and wide-scale travel backdrops. Arguably the monomyth comes first, before the background: although some of the more skilled authors of the sub-genre spin their plots within the constrains of a background world, and sometimes manage to avoid the monomyth completely. (I'd go so far as to say that "Matter" by Iain M. Banks is an almost complete rejection of the form, as is "Look to Windward" ... actually, I suspect IMB had his own different idea of a story structure in mind for the Culture novels: as often as not they're epic tragedies ("Consider Phlebas") or illustrations of the limits of heroism.)
But if you're trying to spin a space opera, and you're reaching for a plot skeleton that works, the monomyth is your friend. Here's an exercise for the involved reader: take my dysfunctional Galactic U professorial marriage from the beginning of this essay and use the monomyth structure to come up with a plot, climax, and ending that delivers a satisfactory sense of closure. You might first want to consider who you are focussing on—the lecherous male prof, his spouse the academic with a dead-and-buried past (she thought) as an assassin, or the grad student with the secret mission. Then you need to consider what stage of the Hero's Journey you are joining them at—for there's no reason to assume the story starts at the beginning, rather than in media res. Next, work out what challenges and allies they might encounter on their way to the climax and resolution, and what role the other characters play in their quest. Finally: what is the prize they're seeking, how do they achieve it, and at what cost? For added points, see if you can find a way to twist the standard Hero's Journey cycle to apply a surprise climax to it—for example, by spinning this steamy menage-a-trois with added murderhate and alien space bats so that it appears at first to be one protagonist's journey but then switches track and turns out to be about one of the others (your classic example of this would be IMB's "Use of Weapons") ...