I definitely had to read up on various tips and tricks to complete the Zeppelin mission! I don't think I would've ever survived otherwise. I was rather bummed out when the Zeppelin in question got into trouble near the end, but after trying a couple of times I concluded that it was probably fated to happen that way anyway. Ygerna was definitely easy in comparison, but she still gave me a bit of a kicking!
And, yeah, it was that battle in the Ministry with Mr Deodatus (well remembered! I didn't) that I was referring to. First time through ED, I got completely stuck here and had to go away and sulk for several months. Though that's a fairly regular occurrence with me: discovering that not every fight in Morrowind was a fair fight for some noob fresh off the boat meant a three month sulk; Bioshock Infinite's daft save system caused me to sulk for nearly a year; The Witcher's encounter with the wolf thingy in the Outskirts made me want to throw my PC out of the window. etc. All my favourite games, but all with a generous measure of frustration.
Ego Draconis was definitely a lot more difficult than DKS. I'm quite ambivalent about the changes made to the fortresses in transition: in ED they were actually quite a lot more interesting than in DKS, but the could be so, so frustrating...