Okay, now I'm actually listening to it (looks like it's an old one you've done before).
Yeah, the flute is indeed mechanical, because the notes are detached. Whether you recorded it for real or not, it sounds too stilted as I mentioned earlier, and it's just how you chose to play it that makes it sound stiff. As for the bass, I do agree with Skrypnyk, it doesn't sound like it's contributing much to the soundscape, and it sounds plain with no distinct articulations. It's as if it's a sine wave, but not quite.
At 0:40, I agree again with Skrypnyk that too many things are going on at once. I hear the piano on the right, the flute on the left, the piano on the left, the bass in the center, the metal percussion on the left, the hi hats, snare, kick... wow, that's a lot. I think the pianos need more rhythmic synergy in the partwriting to sound more cohesive and in agreement with each other, and the flute can be more centered at that point (automation?) to let the left piano come through more.
At 1:36, by "sloppy" transition he probably meant the retuned metal percussion; it sounds too artificial. Also, I see what Skrypnyk means by breakbeat. The drum pattern at 1:39, for example, has a lot of snare fills in a row, and is in the style of breakbeat (not to mention it raises the energy of the track, even though there's ambience at that time as well). If you took those snare fills out and made it more plain, it could sound more downtempo and less conflicting in the amount of energy conveyed.