Jesse Ventura and the other man in black was Alex Trebek 
Was it Trebek? Or was it someone or something that looked like Trebek? Or was it Trebek only he was drugged/mind-controlled so that he would not remember what he did?
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I prefer MotW over long-arc because with MotW you don't have to keep things straight n your head. There's no "wait, who's that guy?" things to remember and with long arc stuff the writers invariably make mistakes in continuity that creates confusion for fans later. And leads to epic flamewars on fan sites about what it meant. Was it a mistake or were the writers giving a clue that will be leading to some revelation later? And what will that revelation be?
Also with long arc there tends to be a lot of characters and storylines some of which always get forgotten as the story goes along. Which leads to the writers needing to prune things later and doing so abruptly and leads to narrative weakness.
With long-arc stories the writers get all excited by all the narrative possibilities but fail to think through the logistical side. And things get left behind. But fans don't forget and if you're binge-watching it's particularly jarring to realize that the B or C story arc you've been enjoying watching has been abandoned.
This leads to the writers having less credibility as the show goes on. Fans start to think, and rightly so in most cases, that the writers are just making this up as they go. And if that's the case then why bother watching at all? If the writers are learning what's happening only a few days before the fans that's not a narrative, it's random bits of plot thrown at the screen.
If I was to do a long-arc story where there is a conspiracy at the heart of the narrative I would figure it all out beforehand, design the villains, their goals, their methods, their support staff and infrastructure, and their limits and then let the audience know these things. Some of it could be explained via exposition on the show but most would have to be detailed online. And updated as their resources change.
And the writers would have no leeway to change any of it. They have to write their stories within those constraints. Team Evil gets no Dues ex machina of any sort. No new super-weapon or secret base to suddenly menace the characters with would appear out of nowhere. No endless stream of henchmen or minions that can killed and so forth (this is one of my main beefs with Person of Interest). To get more resources the process of obtaining them would have to shown and with no hand waving or montages and there has to be a cost paid in some sort of trade-off for the evil org.
Even the most well-funded and capable operations cannot do everything and get stretched thin in places trying to do all their routine things even before the attrition process caused by enemy action. They make mistakes too, and have to deal with non-team players and outright traitors as well as the usual sorts that end up in any hierarchy. Team Evil is not immune to shirking or theft of office supplies or even outright embezzlement. (They would in fact, have to have a legitimate, if evil, HR department. Otherwise they could be brought low by personnel issues) and all of this would have to be reflected in how they respond to threats. Also they are not omnipotent.
The evil org cannot snap their fingers and have exactly the right operatives in exactly the right place every time. There will be times that they have to improvise and put something together on the fly to respond to the actions of the heroes and showing this could and would be narratively interesting.
There would be a lot of drama in the heroes figuring out the plot and the capabilities of the plotters and making mistakes in the process. For the fans it's more immersive. If the fans know that the Evil Minion is bluffing in a certain spot but the characters think he might be but there's too much at risk if they're wrong...you'll have fans screaming at their television sets for the characters to call the bluff and devastated when they don't and miss a huge chance to hurt Team Evil. Both sides can be shown to be utterly confused by some event or fail to react to or even notice something the other side did.
And from there you can and must build short and medium arcs for both sides as they react to events and adapt to changes. Team Evil lost a base and some key personnel, what do they do to rectify the situation? Team Good's best forensic accounting guy loses his wife in a traffic accident and now the analysis of some financial activity has been thrown into disarray. What now? Was Team Evil involved? Team Evil needs to do something in a town they have no operatives in and so they send a team there but the computer guys get snowed in in Newark and the op guys need to hire locals but can't tell them what's going on and they can't dispose of them afterwards for some reason or another all the while trying to stop or delay Team Good and the plumbing just broke...
All of this would be layered with MotW episodes. So it's not all conspiracy, all the time. Which isn't to say Team Evil won't try to take advantage of some of these events but sometimes the MotW screws over Team Evil.
You could keep a well-written show like this going for years.
