Admittedly yes, the series has lost it's serious grounded story heirarchy. From my perspective, this is primarily due to 343 and their lack of willingness to support, recsll, retell and otherwise work with previous lore/stories, and instead forge ahead while developing their own sense of story within the Halo Universe.
However, I do have to acknowledge that for the past 15+ years, we have become acustom to a "Covenant vs Human" storyboard heirarchy. It would simply be a logical progression of our thinking when it comes to Halo, to dismiss or becone dismayed by Hal's own inevitable ending of the Great War to make way for the next decade of historical and menirable combat driven storyline.
The main problem is, 343 has shown twice, how utterly incapable they are of creating original content to push Halo beyond the established borders of what we expect. I would believe that if Bungie had not left the franchise, we would have seen a very different Reclaimer Saga, and ones who progression in both story and multiplayer would have placed Halo back at the top if the FPS genre.
Now that last part may simply be an opinion, but it is an opinion based soley upon the previous developers work, dedication and slready proven results, weighed against what we now see.
As for the scientific aspect, I draw my conclusions and debunks from the data that the actual lore has provided, versus what we actually do kniw acording to real world physics. For the most part, Bungie and 343 fill in no blanks and provide nothing in terms of inner workings, explinations or any other attempt to validate the technology.
As a point of reference, look at Star Trek. The entire concept of Star Trek back in the 60's proved widely impossible. Yet, the writers and Roddenberry did a supremely wonderful job of referencing actual physics and space-time mechanics to validate the possibility of such events, and further they actually cant much be argued wrong or simply hypothetical. For another reference point, look up the technology used in the series. You will find blueprints, schematics, technology overview pages and fictional interviews. Then look at Halo. You will find nothing but half concocted "it just works" explinations, and a ton of incorrect scientific, physiological and genetic data with wildly incorrect explinations.
To end this already way too long post, the series isnt credible anymore and it hasnt been since Staten stopped being the end all be all of story telling for Halo. If the series wishes to be what it was story wise, 343 needs to be more honest about their failures, their shortcomings and dedicate themselves a lot more to ground themselves into a more stable story heirarchy.