Having a truly epic battle is a cornerstone of fantasy gaming. Obviously a big part of that raw numerical difficulty because if the boss just falls over it doesn't feel exciting and if you all die then boo sad times! The epic battle should be hard and taxing but winnable. That isn't all an epic battle requires of course - mood and buildup are a key component to making it feel powerful and awe inspiring. I actually really like the way this recent DnD Next article talked about dragons - rather than just listing stats they talked about the inherent magic of the beasts, how they corrupted the world around them, and what it would be like to approach the lair of a powerful dragon. The descriptions gave fantastic background for a GM to build what is almost a dungeon crawl through the wilderness to actually get to the beast in the first place which is especially effective because each dragon is very different. Thumbs up there for presenting dragons effectively as terrifying monstrosities instead of 'bag o loot and XP'.
I think it is very much worth considering how many special mechanics you want to devote to boss fights. Back in earlier editions of DnD there wasn't anything like that; in theory at least the monsters were built off of some kind of simulator instead of kludging it to make the numbers work. This is, of course, why the numbers in 3rd edition and earlier were completely borked and the numbers in 4th edition were much more reasonable. 4th edition also had all kinds of very gamey mechanics to make building bosses work better like Action Points, Hit Point multipliers from nowhere, Saving Throw bonuses for no reason, etc. This is why 4th edition fights were so much easier to design and run and why they never ended on round 1 with a lucky crit.
It is unclear to me how much of that I should incorporate into Heroes By Trade. I definitely don't like the DnD 3rd edition style where monsters are built by directly using their stats and Hit Dice and such because it always ended up with monsters with defenses that were way too high, Hit Points that were way too low, or other glaring problems. I really prefer to simply be able to say "Well, an Iron Golem has a bajillion HP for no reason at all. They are tough, who cares?"
The major difficulty I faced was figuring out what to do with debuffs. Randomly Stunning an opponent and negating their turn is not unreasonable when the fight is a 4v4 brawl - clearly the Stun is useful but it can be sensibly costed. If high level characters can toss out lots of Stuns though a boss that isn't immune to them is going to be utterly helpless. What I am wondering about is whether or not I should create some rules subset for powerful creatures to be resistant to the most debilitating of debuffs. It is possible both for the monster entry or the GM to simply make particular critters immune to particular things and this does feel a lot less kludgy than slapping a 'boss template' on something. Encounters that have been so obviously altered tend to not have the epic battle feel that people want. They want it hard but they want it to play by the same rules they are used to. With at least a couple of very nasty surprises thrown in, naturally.