Or those boss fights where you have a central boss and peripheral parts which you can also attack but which respawn some time later if the main creature is alive. Do you just go for the boss, or do you whack the hands first to reduce his damage output and resistances?
Another issue is planning. Make the dungeon like a heist movie. If you just blast your way in, you'll have a hard time. But if you investigate, scout, plan ahead, gather resources, you can execute your plan and maybe not even fight the boss.
For example, maybe the dungeon has some shortcuts that you can't use because they're sealed. If you find the magic required to break the seals you can sleaze your way through the dungeon. Maybe if you research the cult's passwords and secret handshakes you can disguise yourself and sneak past most of the trouble. The boss itself might just be a treasure guardian which you could bypass fighting if you snuck into the cult leader's quarters and stole his keys.
If your PC doesn't have the skills necessary, he could hire someone to come along, or learn them.
Bringing this back to the issue of spell variety, rather than specific spells to break the seals, each seal should have a code of spell effects that you need to cast in order to break it, like a combination lock. Maybe a landslide / cave-in requires a Dig spell plus Wall of Force to reinforce the passage. Or a hall choked by poisonous plants could require Protection from Gas to approach close enough to use Charm Plant to get them to move out of the way.
There are lots of ways to learn the cult passwords. Charm Person and interrogate. Mind Reading. Crystal Ball to see and hear from far away when the cultist uses them.
You could use all kinds of different tools to get into the cult leader's room and steal his keys.
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Also, there are ways to make the status ailment spells less useful. In a lot of editions of D&D, for example, the low-level Sleep spell is great against most enemies but if the target is over 4th level it doesn't affect him. Hold Person is low level and affects a few people, but most monsters don't count as a "Person" and you need the higher-level Hold Monster.
Another restriction is that you typically don't get a lot of these spells at once. It's not like FF where you can cast your best magic throughout the fight and quaff an Ether or three and keep casting. Imagine a FF where your spell points are a resource that you can't recover during a fight and you have to leave the dungeon to rest or heal, and a Potion is something that a powerful character might have one or two of. In a standard JRPG and most western CRPGs, your resource management is very short-term, sometimes to the extent that you only need to worry about what happens in each fight independently because you'll get everything back at the end of the fight.