people often bitch about the metaplot (i know you guys arent, im speaking generally), but i kinda like it.
i mean, i dont like it that its changes so sweepingly over different editions of the game. but i chalk that off to revisionist history in the imperium.
i do like the first edition metaplot, and how the third edition crap with the necrons and the ctan and the war-in-heaven brought the old ones back into it. i like the suggestion that the tyrinid swarms are old one psychic / bioweapons (they were masters of bio-engineering after all) sent from another galaxy (the old ones did disapear and were thought to have retreated to another galaxy, after all) to fight the ctan (who are specially vulnerable to psykers, after all).
i dont really like the idea of missing or lost chaos gods. the whole metaplot behind chaos and the warp is that its supposed to reflect the emotions of life forms in the physical world. it was stable until humanity spread across the galaxy in the golden age, and only destablized once enough of us were out there thinking bad thoughts to have a negative impact on it.
chaos gods exist because people will them to exist. if the emperor is a "lost" chaos god (i prefer him as an old one, but whatever) then it sort of shits on the idea of gods being reflections of our subconsious. if he is just a man with the powers of a god, its because the collective will of the imperium of mankind (along with all those sacrificed psykers) wills him to have godly powers.
anyway, just my two bits.