When you make a theory,first: Not everything is necessarily meaningful inside the manga. For instance,Natsu and Acnologia look similar,but that was probably made only to accentuate the contrast between them. Natsu is a dragon slayer that doesn't kill dragons,Acnologia kills even his comrades. Natsu fights for others,Acnologia fights only for himself. Natsu said that he would have gladly become a dragon to protect his friends,Acnologia became one for kicks,etc. To say that they are related solely because of appearance is to say that Kyouka is related to Mirajane because she looks similar to her Satan soul.
Second:You base yourself on what the manga says. The manga clearly explained that Natsu was created based on Zeref's dead brother. That eliminates the possibility that Acnologia and him are two parts of a whole or something of the sort. A pity,I really liked this theory.
Third:Even if the manga doesn't say so,one can still try to make theories,but well,the ones that tend to be right are the ones that require the least assumptions. Even this isn't absolute.
Wait a second...To bring back the dead,there must be a suitable and equivalent exchange. This probably works like fullmetal alchemist,except that in here either there is something of equal value to a life,or it's possible to sacrifice a life to resurrect another. In fullmetal,each life was unique,so there was no equivalence between them.
also,Natsu was probably put in suspended animation. If the dragons could have created antibodies in 14 years,they could have attempted it in the civil war. It probably took 400 years to make them. The eclipse is a good possibility,but...Natsu and the others didn't awake in the same place at X777. Plus,Fried's runes recognized Natsu and gajeel as being older than 80. if they time traveled,this shouldn't be possible.