So I played through this game in one sitting (~3 hours with an additional hour or so afterwards for the secrets with a walkthrough) and it was what I would call a satisfying experience. It plays a lot like Limbo did with improvements here and there while also managing to fall short here and there. The game is very atmospheric, just like Limbo, but it's also pretty same-y throughout where Limbo just tended to feel like it had more variation. Still pretty dreary stuff at the end of the day, though. I think the game improved in that it isn't constantly trying to kill you in some fun to watch way. It isn't constantly trying to make you fail like Limbo did. The puzzle mechanics tend to be imaginative but tend to get overused juuuuust a tad before it moves on to a new one. I would say only one puzzle was badly designed, though.
The story is... even more vague lol. Like Limbo you really have to make a judgment call on what the ending means with the clues the game gives you. The thing is, this time it's a little more difficult to discern than a boy stuck in a loop in some form of Purgatory.
Ending theories:
There are ways to take both games literally as they are shown to us in the games themselves and there are also ways to take them as metaphors. I think Limbo by itself is a representation of Purgatory and the boy is stuck in a loop. There are also ways to take Inside as a metaphor for all kinds of shit... I don't think it really connects to a single metaphor quite like Limbo did. The metaphors people have come up with for Inside also kind of make me want to roll my eyes. In any case, taken as more of a literal game I think Inside is a sort of prequel to Limbo. The anti-gravity mechanics and mind control worms all kind of seem like prototypes to what can be seen in Limbo. For example, by the time Limbo takes place there's a creature that seems to specifically prey on the mind control worms. There's also the piles of dead pigs and people that seem to refer to failed experiments.
The kids connection to the blob is one that I have trouble making conclusion about. My favorite theory is that the kid is always a part of the blob and the is being drawn to it. This is supported by the way the zombies seem to want to help him and him seamless integration into the blob once it is free. I'm not crazy about this theory as a whole though. I think the most interesting part of the game is how powerless the boy is until the naked swimming girl plugs him into that device briefly as she takes him deeper into the water. I can't really speak to her origin so her objectives are hard to guess at.
The alternate ending can kind of pinpoint this theory though. You get the ending by getting all the secrets. All the secrets are those orb-y things that once you deactivate seem to cease the functionality of the mind control power-thingies. This is supported by two instances when you're disabling the secret orbs - one orb when deactivated makes the mind control hats useless and seems to just kill the two zombies nearby permanently. The other instance is where you're being chased by dogs and when you get the orb deactivated the dogs lose all interest in you (suggesting the only reason they're hunting you is the organization's mind control). It's also supported by the ACTUAL alternate ending itself, where when you go under the corn field and open the secret ending door and unplug that weird prototype-y looking mind control device you yourself slump over like a zombie. (Edit: Saw like a 0 second reaction to the alt ending in a Twitch stream where the streamer thought this was more of a reference to how the boy is being controlled... by you! The player. Kind of like how the boy controls the zombies, you were controlling him. This probably works better than my ideas)
The alternate ending kind of supports the idea that the kid is linked to the blob in some way. I'm going to guess that the blob is the culmination of their efforts in.. mind control and whatever else they're doing. The fact that the weaker zombies deactivate when the small orbs go down and the boy only slumps over when the alternate ending plug is pulled makes me think that he himself is some sort of prototype that when connected to the whatever by swimming girl is able to do all these special things. I think the prototype is somehow more powerful then the blob while simultaneously being the same kind of entity which is why when the boy is seamlessly absorbed he (as in you the player) still has total control.
As to why the workers at the end (who seem different than the people who are trying to capture/kill you) help you escape.... Ehhhh I'm not really sure. Maybe they realize all the evil shit that's going on and want to do their part in ending it? Maybe they realize you and the blob are a failed experiment and the only solution is for you to exit the facility. Once free and you finish falling you lose control. Are you too away from the mind control devices and cease functioning, maybe too far away from even the prototype device? Or just exhausted from the exertion. I think this part of the ending is justify in a literal interpretation... It's left open ended and will probably never be addressed. What was accomplished is probably the question I would like answered most of all about this game... that and the swimming girl.
The ray of sunlight on the blob is reminiscent of Limbo but I don't even know where to begin with that (and doubt I should).
tl;dr ending theory
The boy and the blob were inside and wanted to get outside. So they did.