Playing through both games concurrently and this is how they compare. tl;dr, the original PoE is the better game.
Deadfire has considerably better quest design than PoE. There are more cool setpiece quests like Arkemyr's Manor or Fort Deadlight, and these typically offer alternative solutions. There are a lot of quests that feed into other quests, particularly in Neketaka. Companion quests, however, are remarkably bad. I suspect Sawyer decided it would be too expensive to implement quests for companions the player might not even use, when they could instead focus resources on the aforementioned setpieces.
Deadfire's stealth is considerably better, for a few reasons: enemies patrol their areas instead of being stationary, encounter density is reduced, and the game better communicates NPC vision. It's actually feasible to stealth through places like Arkemyr's Manor, however there are many places where you're forced to fight, e.g. Hasongo.
Most of the changes to combat mechanics in Deadfire were bad. I already mentioned my distaste for everything being per-encounter a few posts ago, but it gets way stupider than that. The overhaul to buffs and afflictions is over-designed, and makes different abilities feel less unique. It also contributes to the graze problem of everything feeling mushy without hard counters. Penetration is an awful mechanic that dominates gameplay and never feels good to play around. You're heavily penalized for being short even 1 point, but you have to DOUBLE the enemy's AR in order to see any kind of damage bonus.
The addition of multi-classing and sub-classes for all is obviously a huge point in Deadfire's favour. It's also rather nice that you can preview the ability tree outside the level-up process, which for some reason Obsidian never considered doing in the first game.
Deadfire also easily trounces PoE (at least pre-WM) on itemization.
Deadfire has a lot more bells and whistles to make it look like a AAA game, including dynamic lighting, more cloth physics, parallax layering, and idle animations. Honestly though, I think the first game actually looks better. I remember Sawyer talking up the skeuomorphic UI design for the first game, and it was a really nice touch that made the game feel cozy to play. Then they promptly dropped that idea for the sequel and went with a boring modern look, probably thinking it would be more console-friendly. Also, there's only one loading screen in Deadfire, and it's worse than every single region-specific loading screen from PoE.
Deadfire's "improved" presentation also comes with a big performance hit. Booting up the game on an SSD takes a solid 20 seconds to reach the main menu, and in-game loading screens are just as regular and slow as in the first game.
Deadfire's companions were a huge downgrade from PoE. I wouldn't say PoE had great companions by a long shot, but I like a few of them (incidentally none of the good ones were included in Deadfire). There isn't one Deadfire companion that I'd take over a hired adventurer. Part of this is with the improved character-building options, it's obviously more fun to create a full party. But they're also really annoying, even before the pointless romance. And as previously said, the companion quests are half-assed and uninteresting.
This might be personal preference, but I don't like Deadfire's open world approach. Most areas are completely impossible for the first 6-7 levels, which forces you to squat in Neketaka and do side quests for hours. I've read Sawyer bemoaning how the similar frontloading of side quests in Athkatla hurts BG2's pacing, so I have no idea why he did the exact same thing here.
Story is tricky to evaluate because neither game did it particularly well. It's easier to avoid Deadfire's bad story because 80-90% of the game is side quests, but in some ways that almost offends me more. Deadfire provides a clearer motivation for the player's actions, but then does the Bethesda routine of giving you every excuse in the book to not pursue what seems like an urgent mission. I think I have to give PoE the edge, as Thaos's scheme to discredit animancy is somewhat interesting once you know what he's doing.
PoE's narrator is vastly superior to Deadfire's. He's no David Ogden Stiers, but his voice carries some authority and seriousness. I have no idea why they didn't bring him back for the sequel, but going with a woman who sounds like she's 16 was not a good choice.
PoE also has better music than Deadfire. Apparently this is because Justin Bell was inspired by the IE games when composing PoE, and he was inspired by Deadfire when composing Deadfire. The sea shanties make me want to stop feeding my crew.