When it comes to making any encounter I find a lot of GMs often try to keep in mind their PC's abilities. When I say that I mean that they custom build their encounters to be a challenge for the PCs. The NPCs have answers for key strategic abilities the PCs have. While this can work for some encounters, and can definitely be a good thing to introduce a smart or more tactically minded enemy, it's not something I feel most encounters should take into consideration for 'early' encounters with a big villain.
The Enemy Probably Doesn't Know What The PCs Can Do
When it comes to first encounters, unless the PCs are particularly famous, odds are the big bad doesn't know who the PCs are and what they can do. If there is already a connection, or the villain is specifically targeting these PCs after having done research then just disregard this whole post. You're already in the exception.
However, when the PCs aren't being specifically or knowingly coordinated around by the enemy, instead it is better to make encounters without considering what the PCs can do to defeat it. Instead look at the resources and approaches the villain has open to them, and build an encounter that way.
How Does This Villain Solve The Problem In Front of Them?
Let's consider a Necromancer villain trying to take over a village to turn into a base of power. The necromancer doens't know there are PCs in the village. So how does the necromancer approach the problem of taking the village? What resources do they allocate? What problems do they expect?
Odds are this is a basic problem that can be solved by the basic approach of "I'll just send a hoard of skeletons at it." And this is a good approach and one that will work 9 times out of 10. There's no reason for the villain to plan around there being 3 cleric PCs in the village. And those cleric PCs will make the fight very easy with their Turn/Destroy undead abilities, but that's fine. It lets those PCs feel powerful. The Necromancer suffers a defeat. And you're off to the beginning of what can be a great (if not friendly) relationship with a new adversary.
The Danger Of Prepping Everything To Deal With Your PCs
The danger of ignoring this, when everything is built to deal with your PCs abilities and skills, is it can rob your PCs of there moments of feeling powerful. More dangerously, it can make them think their abilities are useless, or - even worse - that you are cheating to make them feel weaker or not let them use abilities you told them they could have because you don't like them.
In short, it can look like you, for out of game reasons, are stacking the deck against them which in turn makes things harder to enjoy. Perhaps more importantly though, if every encounter is custom built to work around key powerful abilities, you can never make an encounter feel special or an enemy feel particularly clever/prepared, when they have a plan to take the PCs down.
Let It Work And Learn From It
Instead I recommend you let the PCs plan work, let them use their abilities, and have the enemy learn from it. If an enemy escapes having been routed approaching with 5 thugs from a fight, maybe next time they show up with 7. If their hoard of monsters got taken out by large AOE spells, maybe they instead send a small, elite team to deal with the PCs that are prepared for those large AOE spells. Make it a relationship where the villain makes an attempt, maybe fails but definitely learns, and then revises their future attempts with that in mind.
Play Into The PC's Strengths
Also take some opportunities to play into the PCs strengths. Show them what they can do when they line up their abilities right. You have a Paladin with a Dragonslayer sword and smites that devastate undead? Let them fight an undead dragon and really go to town. It lets them feel heroic. Let's them have that crowning moment of awesome. And when they feel strong, they'll play into future encounters.
A bunch of PCs too scared to engage a foe because they're waiting for the trap to close isn't something I consider fun - and no offense if your group loves it. PCs who know they may need to flee some encounters, but also that if they have a clever idea/approach it'll work though? That's where you get people thinking. And that makes for some VERY fun encounters.