The problem with a lot of your points is that back then, the extended fiction was mostly just a kind of background bonus for those of us that really enjoyed the lore. If you only played the games and hadn't read any of the extra stuff, Halo 3 did a decent job of finishing things off while also incorporating some interesting bits of lore that were cool to speculate about such as the terminals. It wasn't perfect and I agree with your points on Truth and Miranda, but at least everything was there that needed to be. It also did finish the fight. The fight that had been going on for 30 years was ended. Yes there is the issue of what would happen to other factions but that is cleaning up after the fight or a whole other fight itself.
Sure, the Covenant battle was finished, but the battle with the Flood was outright stated in the final level to only be on a delay. The Gravemind promised his return and looking at the recent
it is probably going to happen very soon.
Halo 4 by comparison started off promising and then ended with more questions than it answered. If I hadn't read the books I would've been completely lost because even with that knowledge I had trouble understanding certain things. The Didact completely failed as a villain if you only played the games in my opinion as there is little to no explanation to who this guy is and what the hell is problem with humanity is besides (what seems like) space racism. I mean even the terminals which contain IMPORTANT information are hidden away and require you to go to a completely different app/site to watch. There's just so many things that aren't elaborated upon at all or even eluded to that it creates a massive mess for those trying to piece it together and that is not good story telling.
I did state this that the main issue with Halo 4 was that it was too reliant on the EU, in regards to the Didact's motivations in particular. Raising more questions than it answers is not surprising since it is the first game in the new trilogy/saga, it never promised to finish the fight so to speak.
As for the questions not being answered, I had a couple of ones mostly in regards to Cortana....
1. Is she truly dead? This type of question could not expect to be answered in Halo 4 anyway, since it is dependent on the actions of 343i in future media. I had recognized her death or loss in game though.
2. What drove the Didact to hate humans post Halo event in the first place? I think the issue here is that Silentium went over this in relative depth while Halo 4 didn't touch on it.
These were the two main questions to be answered in Halo 4's story, in my humble opinion. Certainly not as many as were left in Halo 3, and let's remember that Halo 3 was the end of a trilogy and not the beginning of a new one.
Similarly Halo CE left a number of plot points open which lead to Halo 2.
TL;DR Halo 3 at least managed to wrap up most of the threads within the established games universe while hinting at some interesting bits.
Halo 4 did very little to explain anything to new and old players alike while creating even more questions than it answered.
Well I'll TLDR my points I suppose:
Halo 3 an asymmetric/imbalance to its story, bad dialogue and characterization at certain points, and failed to finish the fight in all areas aside from the Covenant proper.
Halo 4, while too reliant on the EU, had the best voice acting out of the Halo games next to Halo 2 and ODST, and did manage to tell a story about the state of the Halo universe 5 years on, even if it did open more plot points as it should have since it is the first game in the trilogy.
Therefore Halo 4> Halo 3 purely from a
lore perspective. I'm not even going to talk about the downgrade we got in story complexity in regards to the Covenant, something 343i have seemingly recognized with this new novel coming out this year.