I've taken all your comments under advisement, and I appreciate the feedback. Based on your feedback and some brainstorming on my part, I have come to a strong conclusion: Irrespective of all the minor flaws and storyline issues, at the end of the day Final Doom has two wads (duh). Both wads must be finished in order to complete Final Doom and henceforth the classic Doom series. Otherwise there is no point in having two wads. Why would they put in two wads if the intention was not to complete both? Nor has it been mentioned anywhere that Final Doom gives you any kind of "choice". The only real choice is the wad you want to play first, and it is recommended to play Evilution first because it's easier. Plus, the Final Doom e-manual I read clearly stipulates that Evilution and Plutonia are both part of Final Doom, I mean, you don't even need the manual to tell you that really. I failed to see the obvious, but have now grown in wisdom. And yes, Doom's storyline is really messed up with a ton of contradictions (like the Bible). Determining "canon" is difficult. But storyline was never Doom's priority, it was all about the gameplay!
Though Doom is a really old game, I've not really gotten into it until recent times, with the addition of the mod "Brutal Doom". After completing Ultimate Doom and Doom 2, I'm now getting onto Final Doom. So, as everybody knows Final Doom has two separate stories: Evilution and The Plutonia Experiment. They have no chronological order, they are alternate conclusions to Doom. Obviously, I'd be interested in experimenting with both wads. But in order to "finish" Final Doom and the classic doom series as a whole, is it necessary to complete both of these alternate conclusions, or do I simply pick one conclusion, one wad? I hope I make sense. In other words, does Final Doom allow me to choose my preferred storyline as a means of completion, like alot of modern games do?