Ludonarrative dissonance is a big phrase for when game mechanics and systems interfere or clash with the storytelling in a game. I think Enslaved suffers from this in a rather unfortunate capacity, which is one of the reasons it did not resonate for me much.  
 
Two Examples 
 
1. The Shiny Bits 
 
Ninja Theory strives to explain every bit of gameyness--health bars, RPG advancement, even menus--with in-game reasons. Monkey can only see all this stuff, including helpful objective markers and enemy weaknesses, because Trip's slave crown is broadcasting it into his brain.  
 
But, when the game begins, Monkey is free of this device. Yet every pipe, every metal crag he can jump to is shining like the dickens. There is no explanation for this. It's pure, obvious, THIS IS A GODDAMN VIDEO GAME in your face. That kinda sucks.  
 
2. The Experience Bits 
 
Throughout Enslaved, Monkey acquires energy that he can use to upgrade. Sometimes it's sprinkled in the environment; all the time it's coming from enemies.  
 
But it is never explained. There isn't even a throwaway line, like the mundane, "oh, looks like the energy of former mechs is floating about because that's just what energy does nowadays," or the tragic, "every floating energy sphere is where a person died in the war." Nothing.  
 
Worse, the experience bits make you actively look at environments for WHERE'S THE SHIT? instead of a more Half-Life 2, what happened here? how did it happen? what kind of stories can this place tell me? 
 
That is poor, lazy, destructive design.  
 
The Ending 

Ludonarrative dissonance is a big phrase for when game mechanics and systems interfere or clash with the storytelling in a game. I think Enslaved suffers from this in a rather unfortunate capacity, which is one of the reasons it did not resonate for me much.  
 
Two Examples 
 
1. The Shiny Bits 
 
Ninja Theory strives to explain every bit of gameyness--health bars, RPG advancement, even menus--with in-game reasons. Monkey can only see all this stuff, including helpful objective markers and enemy weaknesses, because Trip's slave crown is broadcasting it into his brain.  
 
But, when the game begins, Monkey is free of this device. Yet every pipe, every metal crag he can jump to is shining like the dickens. There is no explanation for this. It's pure, obvious, THIS IS A GODDAMN VIDEO GAME in your face. That kinda sucks.  
 
2. The Experience Bits 
 
Throughout Enslaved, Monkey acquires energy that he can use to upgrade. Sometimes it's sprinkled in the environment; all the time it's coming from enemies.  
 
But it is never explained. There isn't even a throwaway line, like the mundane, "oh, looks like the energy of former mechs is floating about because that's just what energy does nowadays," or the tragic, "every floating energy sphere is where a person died in the war." Nothing.  
 
Worse, the experience bits make you actively look at environments for WHERE'S THE SHIT? instead of a more Half-Life 2, what happened here? how did it happen? what kind of stories can this place tell me? 
 
That is poor, lazy, destructive design.  
 
The Ending 

Video games, yo.

That's not really ludonarrative dissonance. I mean, it's vaguely like it but not really.

These are the reasons it did not resonate with you? They seem like trivial issues, particularly as the main reason people love the game is for the portrayal of the characters and their relationship through the game.

I thought the game was awesome up until the ending; it just left so many loose ends and stuff that wasn't explained like Monkey's motives right before the credits rolled. 
To be fair about what you said about Trip; she wasn't exactly useless and powerless, she had her gadget thang remember! And I've been thinking, not every female character has to be empowering or "badass". She sort of leaned on the damsel side but she had more depth to her character and I think it worked great. 

The only bit that grates somewhat is the experience orbs. The game doesn't do a fantastic job of assimilating that into the game world narrative. It also fails to explain how Trip (although a computer whiz) is able to repair and upgrade you on the fly. Effectively she acts as the 'shop' in the game and it doesn't sit well.

Apart from that the story is exemplary. The ending is minimalistic, completely open to interpretation whilst at the same time helping to explain much of the story up to that point and at once expanding the game universe with possibilities. It's extremely clever in how it at once completes the story and yet opens up enough questions within the wider game world without necessarily leaving loose ends. It also does a pretty decent job in explaining the cost of freedom, without being moralistic. 

" I thought the game was awesome up until the ending; it just left so many loose ends and stuff that wasn't explained like Monkey's motives right before the credits rolled. To be fair about what you said about Trip; she wasn't exactly useless and powerless, she had her gadget thang remember! And I've been thinking, not every female character has to be empowering or "badass". She sort of leaned on the damsel side but she had more depth to her character and I think it worked great.  "

I think of the shiny bits like they're the color red in Mirror's Edge. Monkey is a master of acrobatics and knows where he needs to go next, so objects being highlighted in the environment is him focusing on his next target. He doesn't see it as a shiny object, of course (that is for the player), but the object in the environment stands out to him, and the shine is a way of conveying that to the player so they know where to go next. Faith doesn't actually see red when she's running about, but those things stick out to her, and the red color is a way to convey that to the player, as well, though you can turn it off if you wish. 
 
I'm not sure if I am explaining this properly, but I am super tired and not editing this!

Nitpicking is fun, my turn!
 
1. Monkey is supposed to be this amazing, iconoclastic loner who has learned how to best survive in the wastes. He's even called Monkey due to his acrobatic prowess. His eyes can very quickly hone in on climbable areas, to help pass this information on to the player (who is not Monkey, and does not posses Monkey's innate or learned abilities.), the ledges glow. 
 
I'd love to rewrite the second point, but I feel that it requires a slightly different angle of approach.

  2. Monkey and Trip are on a character-driven mission to return Trip home, and then some rank shit. While it's kinda sensical for Monkey to want to grow stronger to fight the mechs in the way, at no point do we learn why the hell these floating things help him become a healthier, better fighter.

" @Scapegoat: Just one of them. Didn't want to talk too broadly. Others:  Fighting becomes boring, then becomes something you dread.   Pigsy is a terrible character in this; his DLC is somewhat redeeming.   Trip has potential to be interesting, but just plays the Emotional Needy Woman role. At the end, she kinda saves Monkey, but it feels like a cheap turn.   Monkey is basically a loner character who has no interesting backstory or motivations.   The subtle change from Slaver-Enslaved to Friends is poorly done.   Nice animation and good writing do not fix these problems.  "

" Nitpicking is fun, my turn!
 
1. Monkey is supposed to be this amazing, iconoclastic loner who has learned how to best survive in the wastes. He's even called Monkey due to his acrobatic prowess. His eyes can very quickly hone in on climbable areas, to help pass this information on to the player (who is not Monkey, and does not posses Monkey's innate or learned abilities.), the ledges glow. 
 
I'd love to rewrite the second point, but I feel that it requires a slightly different angle of approach.

  2. Monkey and Trip are on a character-driven mission to return Trip home, and then some rank shit. While it's kinda sensical for Monkey to want to grow stronger to fight the mechs in the way, at no point do we learn why the hell these floating things help him become a healthier, better fighter.

Your abilities would become arbitrary Deus Ex Machinas without the orbs bestowed upon you at random when the designers felt like doing so. There is never any mention of Monkey -wanting- to grow stronger to survive the journey or protect Trip, rather the experience orbs that drop from Mechs represent the inherent increase to physical strength that comes from a physical activity (crushing robot skulls), the ones scattered around the areas could easily be explained by the fact that pulling himself up and along ledges, Monkey's muscles would rip and rebuild themselves even stronger. The Orbs are there to make the progression of Monkey seem more gradual rather than just dumping abilities and stat boost on you randomly between levels, which at least in my opinion, would be even more 'gamey' than the Orbs. "

No... All games have forms of currency that are never explained...

Has it ever matched? I need to rescue my wife from a supernatural force, I need to explore this vast underwater metropolis, I need to hunt down a former ally across two countries; All of them are achieved by shooting fools in the head.

Yea, the ending really sucked. Felt like a hard slap to the face tbh.  
 
I also agree about the shiny pipes. I hate when games are that obvious. At least do it like Uncharted does it and use color and contrast instead of giant flashing signs that scream "CLIMB ME!"

I know big words, too.