flametitan
Explorer
Yes. Missile weapons and focus fire. Also stealth is good.
My players' first encounter with drow was when they ventured into the caverns below the surface and ran into eight or nine drow (one Elite Warrior and eight regular drow IIRC) in the dark. The drow had 120' darkvision so advantage on all their attacks (which cancelled out disadvantage for being at long range on their crossbows) and the Necromancer's dozen or so skeletons had disadvantage to shoot back. The drow wound up knocking out both the Necromancer 9 and the Shadow Monk 6/Druid 3(ish) with their sleep poison and hand crossbows; they took enough casualties that they didn't stick around long enough to finish off the downed PCs in the face of skeleton archer counterfire, so the Necromancer lived (made enough death saves) while the monk died (failed three death saves).
Other things that necromancers hate include bad terrain (have to jump this 15' canyon or take 4d6 falling damage? 4d6 is nothing to a PC, but 4d6 to each skeleton really hurts), infiltrating populated areas (trying to sneak 4 PCs into the Mind Flayer citadel is far easier than sneaking in 30 skeletons or 30 mercenaries), and monsters who are good at hit-and-run attacks (a white dragon who smashes 12 of your skeletons and then flies off to short rest and regain HP). Having skeletons means you're basically giving up the logistics of a PC Special Ops team in exchange for the logistics of a platoon or small company. If you as a DM design your adventures in such a way that a Special Ops team is the logical way to approach problems, necromancers and other minion-oriented PCs will self-limit. And you'll have a better game, because you'll finally have an answer to the question "Why is the King giving this quest to me instead of to his army?" This approach isn't really compatible with the "lots of easy encounters" Combat As Sport adventuring day meme, but it's perfectly compatible with the Combat As War paradigm.
I'm also thinking AOE also works if you're 8-9th level. Remember your ability to command skeleton is limited to 60 feet of you. With average hit points, even the extra Wiz level to hit points means they'll be one shotted by a Dragon breath regardless of success or failure (Though if somebody has the leadership feat, this is mitigated to being one shot by a failed save.) So this range limit does put an upper bound of probably around a dozen skeletons.
Additionally, I also noted the ability to reassert control has to be done before your control ends, not when it ends. This means that ever so slowly, the time you have before you can reassert control creeps back to before you can complete a long rest, which means you run the risk of them eventually turning against you in your sleep. This one is a bit easier to mitigate, however, and more of a pain to manage, so it's not the best balancing factor.
I do like your analogy to special ops teams, though. It does describe a better way to set up D&D missions, when abilities are balanced around the dungeon environment more than for the outside world. I do feel like the importance of 6-8 encounters to balance is overstated, though. 2 short rests per long rest seems to be the more important factor than how many specific fights you get into.
But this is all off topic to the Bladesinger.