Okay, in my opinion:
1) The backer NPCs: not
that big of an issue, as you can safely just ignore them. But it's great that the sequel won't feature them in such a way.
2) The visual aspect: the biggest problem here is how the visuals, especially when it came to combat, seemed confusing and chaotic. Clusterfuck-ish
Comparably, the IE games never suffered from this. PoE2 looks like (at least in those videos and gifs they showed) they're well on their way to fix this.
3) The main story: like you said, there was a clear disconnect here. It was to be expected considering how little time they had to make an entire game (and system) from scratch, but it's still pretty weak.
4) Stronghold: they expanded it a lot with the added quest and other companions' adventures.
Apart from that, I think they correctly identified the biggest weaknesses of PoE1:
- Lack of visual clarity in combat.
- A stronger (i.e. - more cohesive) story with a central idea and vision behind it. Unlike the first one, they had a lot more time to pre-plan and plot this one out, and Josh is personally going to go over all the quests to ensure there's not another Cipher/Watcher lore confusion like in PoE1.
- Factions being an underdeveloped afterthought. Here they're promising to pull a Fallout: New Vegas regarding them.
- Companions having little personal agency in the story. In PoE1, the only companion (as far as I know) who could attack you was GM, and only when you wanted to hurt a child in a certain quest. Again, they're going the F:NV route here.
- A greater motivation for the PC to care about (and participate in) the main plot.
- More (and better utilized) skills. I forget the exact number they said, but more than 10 skills will be in the game.
- More scripted interactions. TWM alone had a lot more than the entire base game, and they were pretty fun and appropriately old-school.
- Better enchanting. Josh said that you'll be able to improve the quality of the gear only one level (so, for example - from fine to exceptional), and that, likewise, you'll be able to improve the enchantment effect on it once (so, for a burning weapon - from flaming to inferno).
- Fewer trash mobs, encounters more similar to the ones from TWM. Self-explanatory.
