My opinion on the whole science fantasy thing:
To start off I want to go ahead and say I think Halsey's Journal from Reach was the epitome of Halo writing, especially because it went so far out of its way to bridge some connections and tie up loose ends. Scientific explanations were concise and didn't rely too heavily on real-world fact or fiction when tech was unrealistic. For example, it illustrates the mechanics behind a Jackal Shield: it's made up of three parts. The gauntlet, a middle portion (labeled "power source?") and the shield generator itself. It utilizes a very basic magnetic field to project a plasma-based energy shield, much like the Energy Sword. The brilliance is in its simplicity: it's a lone magnetic field. Two poles, all in a radial or elliptical shape, which is why the shields are just a basic circle. The magnetic poles account for the small holes on the shield in the games.
It goes into some trickier tech, too; Halsey examines a Plasma Repeater, if I'm remembering right. She goes on to explain that the Covenant deliberately don't want people modifying their tech - weapons disassembled for examination tended to explode violently to prevent tampering. She also points out that, mechanically, their guns don't make any sense - on the inside, things like batteries, ammo pools and heat sinks aren't even visibly connected to firing mechanisms. It simply leaves the explanation at that. No convoluted attempt at justifying (MAGNETS BITCH, etc), no genesongs. It's a good way to illustrate that the Forerunner tech (which is the basis for all Covenant equipment) is just in a completely different league, illustrates their power, and still keeps them mysterious. Well done, Nylund.
By contrast, there's Greg Bear. When I think of Forerunner justifications, I was expecting something similar to how Metroid handles it. There's not too much physical science behind it, but the canon numbers that exist are extreme. High-density neutrino beams, semi-automatic explosive mortars operating on nuclear fission, plasma reduced to close to absolute zero kelvin to create Scattershot-like ice weapons.
I don't think the problem lies in the Forerunners being out of a fantasy novel; in-game, the Didact looks spectacular using 343's design philosophies. My first impression was that his suit looked a bit like the biosuit from Crysis if he were a paladin. This is to be expected, though. The Forerunners have almost always been treated as space hippies - powerful ones for sure, but space hippies nonetheless. I think the problem lies in the fact that we're treated to a few very foreign concepts that don't have any potential scientific backing by themselves. For example, look at Genesongs. The name alone brings to mind some more fantastic elements of fiction. It would only take a few lines to dissipate each of these complaints; instead of some basic statistical data, we're getting proverbs, which is where the issue stems from. For example.
"Out of the Didact's sight, I planted seeds. Your physical augmentation. Your combat skin. Even your Ancilla, Cortana. You are the culmination of a thousand years of planning."
If you leave audiences with just this line, suddenly Chief is space jesus. He's the chosen one, all of that. Yet all of these complaints can be rectified with just a little bit of science to the Librarian's apparent magic.
Chief: "Are you saying I was chosen for this?"
Librarian: "No, human. The Forerunners experimented heavily in genetic evolution and physical augmentation - mutation - to further enhance our abilities to combat the Flood. Much like the recruitment programs attempted by your race. Through what remaining power I held, I attempted to assure the survival of your degenerated race. We call them Genesongs. Seeded into the remaining specimens of your ancestors, I desperately hoped that some day the evolution would bear fruit - and I see now that it was successful. It offered humans another chance to rise and continue our legacy."
Chief: "And Halsey - were you responsible for her?"
Librarian: "She was simply fortunate enough to rise into a position of power, much as you did. There were thousands of lives before yours that showed potential - evidenced that our decisions were not all for naught - and thousands more will live and breathe with that same potential long after your purpose is fulfilled. You are simply the keystoke of your generation, and you will certainly not be the last."
Bam. It keeps the cryptic philosophy of the old forerunners, ensures Chief isn't space jesus, doesn't burn itself out trying to scientifically justify everything.
Oh, and 343? Keep the Didact's fucking helmet on for the entire trilogy if you wanted to keep at least a semblance of their mystery.