(First of all, I played the Polish Tension version a while back, so I'm not sure about the English terminology, how it fits with the rewritten story, or if any details as I recall them are accurate.)
About the endings: I think that the main problem is that we're told throughout the game what kind of worlds would the Sisters create once they're freed, but once they are, it all seems similar, except tinted with different colours. I think I may have expected the vision more faithful to their own description. (With perhaps, at the very end, bam! a shot of the freed Sister in, perhaps, casual apparel, strolling down the street (with the player beside them if they went outside too)

- that's probably too straightforward and happy-ending-like, sappy, stereotypical , for a game like this). (I think I'm also not very fond of the ending because my PC was barely enough to satisfy the minimal requirements, and I was running on minimal graphic settings, and even though the loading times were loooong, everything was running smoothly, except the endings which were just a slideshow

I suspect the fancy colours may have been too much, because intro was similar but played OK.)
Well, the superficial meaning of the story to me seemed to be about some kind of afterlife, in which there exists the possibility to break through back if one's crafty enough. I, too, got the suicide vibe from the game, though I can't right now remember any direct arguments for or against this, so maybe I just imagined it. I don't particularly like the heaven/hell/purgatory analogy (perhaps because I'm not religious), and it only fits the vertical tree of Voids in a limited way. (Because it goes like, from top to bottom ??? - ??? - the realm where the Godsend came from - the Surface - the Void - the Nightmare where the Brothers came from - ??? - ??? That means there are more states of existence - and it makes me wonder if realms of basic animal consciousness are included in the tree, or what higher forms of life exist above us.)
It seemed also possible to me that the player's character got stuck in a different sphere of consciousness (perhaps catatonic in the real world as a result of some trauma?) and, again, struggling to break free.
Although the game seems to contradict this by stating that the player is the Void, with Sisters being the various possibilities that a human soul/mind can achieve, ways that one can go, projected by the player's character, the interpretation I enjoy the most that they may have been separate beings. Choosing one of them and feeding her would mean that you can achieve fulfilment through
love - you give all you have (colour) to another. (Also, if the Void is the creation of the player, how come it feels like it existed before - the history of the two Sisters which got executed, which caused Echo's rebellion...) Even though the Sisters may sometimes be deceitful or manipulative, that doesn't mean you have stop loving them... - I don't think the Sisters were meant to be "good" (some, like the Nameless may be very selfless, but others, like Ire, might not) and the Brothers "evil" (rather... lost? not knowing the truth and trying to find it in the world, sticking with what they know because they fear the unknown).
The gathering of colour and painting with it to me symbolizes beauty (inner/outer?) and creation, the freedom of expression. Through creating beauty (I use this term rather loosely - it may be something more direct, like art, but also our dreams, our work, our everyday life - it all can be beautiful in some humanistic way), witnessing it, sharing it, spreading it you can achieve glorious things. You have to realize your inner potential, and go along with what you feel, even though it might be against the wishes or rules of, for example, the society, or simply even if it means overcoming the difficulties of reality (both of which could be represented by the Brothers). Going along with everybody else's wishes instead of your own, not pursuing your dreams, means a personal defeat.
The Void's imminent collapse I think means that everything changes - nothing stays constant for too long, and after some time the current state of things will become something else, whether for better or worse.
Storywise, I think the most complex is the relation between the player, the Godsend on the surface and perhaps Ole - I don't think I remember the details well enough to present a good explanation, but I'm sure too look into it more closely next time.
Also I have to agree with The LxR - some things said in the game are very straightforward instead of a convoluted metaphor. Like, for example, the symbol of the heart - you can have many hearts, because you can be passionate about many things; sometimes you have to fight for them, sometimes you have to search for them, sometimes they are given freely to you. You have to fill the hearts constantly lest the passion should die out. And, if all your hearts get empty - if you care for nothing, if you didn't work enough to sustain your interest in anything - you die/fail.