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Reading the boss design tutorial I wrote 3 years ago makes me wanna punch myself from back then on the pancreas. Or at least gently slap him on the cheek. Gotta rewrite that thing, especially now that I'm more experienced (I guess?)...
Got a link? My game - for all the criticism it gets on just about everything else (and to be fair, that criticism is justified) - I've seen mentioned several times as an example of the right way to go about boss design, so I'd be happy to share some of my thoughts if you like.
Sorry for the late reply!
Here is the tutorial if you want to check it out. It's mostly about generic stuff to do, with the more specific tips being suggestions from commenters:
Maki was my username back then.
Warning: Naiveté; cringe; bad jokes and puns; corny, groan-worthy references; etc.
Not bad advice, really.
I'll give a couple of examples from my game, that get quite highly praised - feel free to take tips from them, or use them as examples, whatever you like.
The first one is the sixth boss in the game; who stands out due to having a different music than all other bosses so far. This boss, Transient, is also by far the hardest boss up to this point - he has around 4200 HP, which is slightly less than the previous boss, but he has a special property where he's usually immune to physical attacks. There's a status effect, Weaken, that reduces defence to zero; it also (the player is informed of this, so it isn't a "surprise side effect" situation) removes this boss's immunity to physical attacks. You can get four of an item, Softening Sand, that inflicts Weaken on him just before the battle, but unless you're quite overlevelled, you won't have any other way beyond this item to inflict it. And after three of his turns, he heals himself of it. You can still deal damage to Transient with magic, but he'll generally get three turns to every two your mage gets. This means you've got to focus on dealing as much damage as possible during those brief windows with the Softening Sands.
His attacks follow a fixed pattern, aside from the target being random. The first move is a physical attack, which deals 100 to 200 damage depending who it hits (by comparison, your party members will have HP ranging from around 350 to 600 at this point). The second move is a magical attack, Pulse, which deals around 200 damage; it can theoretically be reflected, but it's very unlikely you'll have Reflect by this point. The third move is the killer - a whole-party physical attack, Trauma, that deals 300 to 400 damage to everyone. Being a physical attack, you can reduce the damage via Defend, of course, but that means taking time away from attacking. And his attacks in general do enough damage that healing is needed.
So you've got a battle where, with limited turns available to you (your fastest characters will likely be trading turns 1 to 1 with Transient, while slower characters will be 2 turns to 3 of Transient's), you have to balance defending, healing and attacking, all while dealing with only having so much time you can actually deal damage to him (though at least you can control when you get these windows of opportunity).
So, that's the first one. Some 20 or so bosses later - including two which also have the alternate music from the Transient battle - we encounter a similar, but much harder, boss, Dark Transient. His HP is somewhere around 50,000 if I remember correctly - which is about average for a boss at this point in the game - and like the first Transient, he has the immune-to-physical-unless-under-Weaken trait. Except this one also has the same for magical damage and the magical equivalent of Weaken (Meltdown). On the other hand though, you likely have plenty of ways to inflict Weaken and Meltdown by this point, so you're no longer limited by a small number of Softening Sands. Unlike Transient who removed Weaken after a fixed number of his turns, Dark Transient resets after receiving a certain number of attacks.
However, Dark Transient's attack pattern is much nastier than regular Transient's was. His first turn is a physical attack dealing about 800 damage (you'll have about 1200 to 1800 HP by this point, depending on your exact level and which party member), his second turn he uses an attack Taste Of Hell, which does small damage and guaranteed Zombie + possible Poison to everyone (Zombie works just like in Final Fantasy - immune to instant death, but healing moves hurt you). His third turn is Trauma, which like the original Transient does massive damage to everyone - around 1400 on average. His fourth turn is Eclipse, which is a Dark-elemental hit-all spell (not reflectable) that hits for around 700. His fifth turn is another physical attack. His sixth turn is Deathly Rain, which does very small damage (around 100) to everyone and inflicts instant death. You can't get any protection against instant death by this point - aside from the Zombie status inflicted earlier in his pattern.
So in this one, if you don't cure the Zombie status, you can't heal. If you do cure it, Deathly Rain will be a one-hit KO. And inbetween them, you've got a powerful hit-all attack, a hard-to-reduce moderate-damage hit-all attack, and a moderate-damage single-target attack - plus a small bit of damage from both of those attacks themself. Making use of in-battle switching can help mitigate this, but it's still a very hectic battle, even if you're somewhat overlevelled.