In short, the game's replayability is very, very short. You'll get various small flavor changes, but it will mostly just play the same.
Enchantment & Itemization
Apart from that, there's a serious lack of some types of magical items in the game. PoE overflows with magical cloaks and necklaces (both which use the same slot), but has very, very few magical belts, rings, helmets and hats. Two of my characters finished the game with regular, non-magical (but stylish) feathered hats, simply because there was nothing better for them to wear after 50 hours exploring.
The (lack of) Encounter Design
Considering Obsidian's staff are arguably the most experiences RPG developers in the market, I find this point a huge let down. Even the average cookie-cutter MMO out there know how to throw some curve balls. Hell, just look at what Daedalic did with Blackguards, their first RPG ever! That game had a smaller bestiary and fewer classes & skills, yet had dozens of really memorable battles. Where are those in PoE?
Spells aren't interesting
As with many other things in PoE, I look at this spell and see that there was a spark of creativity, but it was never fully developed.
FINAL THOUGHTS
IMHO, there are two ways to judge Pillars of Eternity.
If you're a casual RPG fan, that heard about the Infinity Engine games, or maybe played them years ago and want something that reminds you of those games but with modern design sensibilities, Pillars of Eternity is everything what you wanted. You'll play through it once, have 40-50 hours of fun, with some interesting moments and not a single "Deep Roads-esque" boring slog.
However, for hardcore fans that replayed the IE games multiple times, that enjoy the depth, replayability and freedom of those games, Pillars is lacking.
But, to me, the most worrisome aspect is the contrast between these two perceptions of the game, because they appear to be almost impossible to reconcile. Reviewers considered PoE a title with "countless strategies" (PC Gamer), full of "interesting puzzles and traps, and surprising encounters" (GameInformer), and even "intensely difficult and tactical" (IGN), but here I am, complaining it's too shallow.
My thoughts
I played Baldur's Gate when it first came it - and I loathed it. Nearly killed my self about 10 hours in. So much that BG2 sat in a box in my bedroom for about 10 years before spring cleaned away.
Then some other games came out that were universally acclaimed by RPG "experts" such as KotR, Dragon Age and The Witcher. Oh, how I hated those games. That engine. That Pause button. Those corridors. Party members with their own back stories and even having the temerity to chat amongst themselves and sometimes DISAGREEING with my actions, me, Lord Azlan.
Don't you know who I am?
Lots of text to read on the screen. BORING. Zzzzzzzzzzzzzzz.
When PoE came out, I ignored it. Removed it from my thoughts. I know what I like and what I don't.
I played WL2 and thoroughly loved it. I gave D:OS a try next and liked it so much, but I found something lacking. Lots of potential and interesting ideas -
So I am tossing and turning, worried what my next RPG adventure would be. I played some Batman and Football Manager. Watched a lot of TV.
I need RPG, I need to dream about RPG again.
The first thing I noticed about PoE was the message in the loading screens about people that are colour blind.
Then I found out that when Calisca said she did not feel safe camping in a dangerous cave, she meant it. I started the whole game again and saved her life second time around - you know how that works out.
Overall, I feel that PoE is better than the sum of its part in the same way D:OS wasn't.
I feel the inventory and crafting in D:OS should have been much better, it obviously is, but who ever got round to using it? The inventory system in PoE is a bit confusing - but it works. Pick up lot of loot ala Risen and sell lots of loot. Spend some time trying to figure out if Sabre A+ E+ is better than Club C+ G+.
I did not like that in D:OS you could go around into houses and nick stuff right under the nose of homeowners. I tried that in Raedric's hold and ended up killing Nedmar as he did not listen to my "D:OS allowed it" complaint.
Combat was a bit simple and straightforward until I came across Raedric. The pause button became pretty important. Positioning my mage also became important. Food also.
Storytelling. Oh how my 20 year old self would kick my arse now. I find the storytelling in this RPG fascinating and compelling. Yep, I use the word "storytelling" in relation to a RPG.
Children being born without souls.
I agree with everything felipepepe has said in the OP, but want to end with a Matrix quote "Pillars of Eternity has made a believer of me"