My heroes are like paper...

He probably just flagged the healer to stay back and set him/her to Avoid Combat. Since you were fighting very few enemies at a time, it may have seemed like all the heroes were in a formation, but they really weren't.

Heroes automatically upgrade their armor as they level up. So if your hero is level 20, then he/she has the maximum armor.
Perhaps you were referring to runes? Those can be bought at a Rune Trader and they give you various bonuses like higher attributes, more health, more energy, more armor, faster condition expiration etc. While they do help, they're not really required; for example, I got Legendary Guardian and Legendary Master of the North on some my characters whose heroes either had one attribute-boosting rune or nothing at all.

Skills have a far greater effect on the defensive capabilities of a hero than their armor or runes.

The person who helped you probably individually flagged his or heros around the great destroyer. You can't do much about the hero armor in terms of upgrades other than runes/insignias (much like your own armor) so for the casters yours should be enough. The real problem you were probably running into is the composition of your heros you admitted to having a less than vast array of skills combatting the last boss of the most recent (albeit five years ago) expansion.

The lack of party formations for hero/hench is one of my pet peeves with GW.

Was the Great Destroyer the harder boss? Are there any other challenging situations such as this?

I felt like I jumped into eton wayy too early.. just fresh off the boat with beating the factions campaign... all of those missions were extremely hard for me to stay alive. I had to micro the crap out of everyone and use stupid methods to finish quests.

I was gonna take on nightfall next, but what do you guys think?

Nightfall should be fine if you've completed EOTN. The mobs in EOTN are the hardest, followed by the afflicted in Factions. Also, EOTN without NF heroes, are you mad?

The Great Destroyer was easy for me, but i was already well-equipped (in terms of properly runed heroes with proper skillbars, as well as my own experience and PvE-only skills, which are game-breaking). Pain Inverter and spirits were the only things needed there, apart of vast healing and protection.
Other end-game bosses were certainly much harder for me, given i wasn't experienced or properly prepared.

That said, yeah, the main issue is that you rushed into EotN a bit; it's designed as end-game content for those who already have beaten the main campaigns (or, at least, so it seems). It has pretty much no learning curve, the monsters are tougher and, in general, it's much more difficult than the regular campaigns, taking average level.
Given you're now semi-experienced after beating EotN, and you realise you need to work on your builds (including skills and bonuses from items, both for you and your heroes), you should do much better in Nightfall. However, i would suggest you going in chronological order now, that is Prophecies -> Factions -> Nightfall, unless you totally don't care about the overarching story of Guild Wars - NF contains some spoilers for previous campaigns, as well as some logically implied plot parts.

usually the great destroyer isnt too hard - i do recall players having a harder time with cyndar ( the wurm boss you faced a quest or 2 previous.
Great destroyer - if you have pain invertor that can help alot , especially if he nukes your party when close formation.Ive had 1 hero survive and muyself an rest were dead and pain invertor did the trick and killed him easily - only recomended if your sucidal lol.

Just DONT interrupt the great destroyer and you should be ok.

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