One thing I still struggle with sometimes is trying to decide if the missions will be seasonal or episodic.
For example, think Heroes. Every episode in Season 1 Heroes is really just one story that take hours to tell, it's basically a miniseries.
Conversely, look at season 1 Alphas. At least in earlier episodes, each episode is fairly self-contained, and has less bearing on future episodes. Maybe they unlock a new ally, but for the most part you could watch the season out of order and still be fine. (Sliders actually PLAYED the season out of order, and it turned out fine!).
I tend to think of my missions like a TV series. At the end of the season they'll be increasing their power level, during the season they'll increase power points or get alternate mission rewards.
But the design of each type of mission is very different.
EPISODIC CONTENT
In this mission, everything is wrapped up in a clean shell by the end of the session or mission. There is a problem, a bad guy robbing a bank maybe. The PCs show up, there are complications, and at the end the villain is put behind bars, or killed, or escapes, but there is no further issue, no great mystery. Anyone who missed the session will not miss out on key plot points later on.
Often these are the easiest to style. The villains need less "fleshing out" because they will only last for this one encounter (or session at least). They should have SOMETHING that makes them interesting, but there is less intrigue. There is no greater plan (or if there is, the party thwarts it now.) Villains may need to monologue to give the players the details of their great plan, since there is no time to "show not tell" them this. The highlight of the mission is usually the combat or the dice roll challenges involved in it.
SEASONAL CONTENT
Most of the missions (if not all) are build ups to the main encounter at the end of the season. If the villain is a druid who wants to choke the world in plants, early missions will have you discovering intelligent plants, or lichenthropes (ha ha), and over the course of stopping several of the driud's plans, you ultimately end up fighting the druid himself in an epic battle.
There are more challenges this way- and it mostly stems from the PCs.
For example, a PC who learns they are up against a druid in early missions, may take special anti-druid powers with their first few power points (such as immunity to plant based powers, or something).
Also, your villain needs to work behind the scenes more, since PCs will do everything they can to stop a villain, (especially a major one!) from escaping at any point. Bosses will often be the target of all attacks while PCs ignore the minions. It gets old if all bosses can teleport.
Your villain also needs to have super-security or secrecy. Don't expect that he can secretly be the head of a major corporation like Lex Luthor, because the PCs will tape record battles and bring them right to the police, or use every investigative power/skill to hunt down the villain immediately upon learning of his existence.Even if they can't prove anything, they will publicly attack a villain they know is evil. (What will the police do to superman anyway?)
Remember, PCs are genre-savvy. They often refuse to hold the idiot ball or the hero ball. They will not stop to let a villain monologue, or even stop what they're doing to save hostages sometimes if it means the villain might get away.
Ultimately, I find seasonal content more satisfying as the GM, though both content types are needed to keep balance and pacing good in an overall story. Any thoughts?