I can’t comment on everything because alot of what you say is subject to your opinion and there is no right/wrong answer to them. However, I can try and offer an explanation for some of the issues you raised:
- The lack of separate stories.
Halo 2 was heavily criticised for this by a large number of reviewers and fans alike. People were not happy that Halo pulled a MGS2 Raiden on us and just wanted to play as the Chief. This issue was made worse, like MGS2, where most of the marketing material only showed Chief and the battle for Earth. To quote some reviewers:
“Halo 2 gives up some of its focus from a storytelling standpoint, which becomes especially apparent once you finish the campaign. A great deal of attention is paid this time around not to the humans struggling for survival, but to the Covenant and what turns out to be a major political upheaval within their ranks. You spent the first game indiscriminately killing these fiends–yet now you’re expected to be sympathetic to them and their hatred for humankind.” (Gamespot, 2004 - Halo 2 Review - GameSpot)
(Regarding Master Chief) - "The first game gave you just enough to make his status as “Humanity’s Last Hope” something that truly felt epic and intriguing.
However, the structure and pacing of Halo 2 dramatically reduces his role in the game, to the point of nearly being misleading. Look at any of the trailers, any of the commercials, any of the marketing, and it’s clear the Chief was being touted as Mankind’s savior in its darkest hour — when in fact he’s reduced to a background character that’s barely there for half of the game (at least, that’s what it feels like). And it just seems odd to me to take a nearly iconic figure like the Master Chief, and do anything that might diminish him. (Opuszine.us, 2004 - Can Halo 2 still be a Halo game when it’s missing the Master Chief? (Review) - Opus)
However, that said, the same sources also say:
“To the game’s credit, all this adds some newfound complexity to the story (even the collector’s edition version of the game’s manual is written from the Covenant perspective), and the plot itself is executed quite well.” (Gamespot, 2004)
Furthermore, the Arbiter’s inclusion was also a ‘cover-up’, with alot of these reviews making no mention of the switch to the Arbiter. I think IGN demonstrates this in their review:“Bungie has wisely placed heavy restrictions on what can be revealed regarding the story of Halo 2. In fact, I can only talk about the first three chapters, which center on Master Chief’s arrival to Earth and subsequent combat in the streets.” (IGN, 2004 - Halo 2 Limited Collector's Edition - IGN)
The shallowness of the story can be attributed to the fact Arbiter’s story is no longer separate but I think you’ll have to discuss further your opinions on that. Arbiter’s story is still there but the writers had to incorporate it into the Chief’s story more without taking gameplay away from the Chief. There ARE some slight plot differences if you play the game in co-op with the Arbiter present e.g. The mission Cortana has completely different lines in some sections of the intro as a result of the Arbiter joining the Chief. Ultimately though, Arbiter’s story was almost done at the end of Halo 2 in my opinion, his ‘rival’ Tartarus had been slain so he had his revenge for the beginning of the Brutes betrayal so in Halo 3, the Elites were supporting Humanity until the opportunity to slay Truth presented itself, which they gave to the Arbiter instead of the Chief.
- Truth’s voice change
The Prophet of Truth’s voice change was a result of Michael Wincott not wanting to reprise the role for Halo 3, hence his replacement with Terence Stamp. I can’t find much in the way of primary sources for this but it seems to be the generally accepted reason from what I can find.
- Lack of appearance by the Gravemind (full body) and Cortana change of location.
This is a tricky one, we only saw Gravemind in a cutscene in Halo 2 in a confined location which can all be heavily scripted for performance reasons. Halo 3 also only had him appear in cutscenes but I assume that the lack of Gravemind in Halo 3 is an engine limitation. The only place I can think of where his appearance could be justified is the mission ‘Cortana’ but given his size in Halo 2’s cutscene, how would you make that work gameplay wise? A big open room with no cover shooting a bullet sponge? It’s possible Bungie couldn’t think of a viable way to bring him in.
Cortana was actively being interrogated at the end of Halo 2, with Gravemind being thought to use the logic plague like he did to Mendicant Bias to drive Cortana closer to insanity. Being that she’s in High Charity’s network she could have simply attempted to escape the Gravemind but, given that the Gravemind has all the knowledge of the Flood, he probably was able to hack into it anyway to continue to cause her severe damage and trauma. We see her actively being affected in the message she recorded for the Chief at the end of Floodgate. Outside of Halo 3, extra lore surrounding this has recently been released, showing more of her interrogation and the techniques the Gravemind used against her. Hidden Xperia does a good job of covering this, though I can’t find the source this comes from (How the Gravemind broke Cortana between Halo 2 and Halo 3 - YouTube).
- Less feeling of grandoise in the campaign
I know this is opinion but I agree. For me, this is because the maps feel more constrained than Halo CE and Halo 2. There are some large maps like The Ark and The Covenant but most of them feel restricted and the illusion to me is lost. Take Sierra 117, a lush jungle but you’re still forced and entrapped by the rivers and forced down a certain route. Compare to Metropolis in Halo 2, where the map is also forcing you down a corridor, yet it somehow feels more open, despite not being as open as The Ark/The Covenant or even Delta Halo, AOTCR etc. Even then, some of the more open maps like The Covenant had sections where it felt small, the Hornet section with the game barriers forcing you to go a certain route spring to mind. That said, it did have some ‘big’ moments like Forward Unto Dawn arriving in-game on The Ark but overall, it felt ‘smaller’ to me. Alot of this can be attributed to technical reasons, still experimenting with the engine on the Xbox 360 etc but Bungie doesn’t seem to have discussed this outright so I’m basing this on assumption and personal preference.
I agree again about the lack of exploration of fictional places. For a game titled Halo, the Halo rings had nothing to do with almost the entire campaign. We only spent the last level on an unfinished Halo ring. The Ark was somewhat cool but given the nature and tone of the story, given that Humanity/Elites were rushing to stop Truth, I felt that we never really had time to explore unlike other Halo games. It’s a bit hypocritical of me to say that given that Halo 2 we were rushing to stop Truth from getting the key to Delta Halo but I think it’s probably because, given all Halo’s were on standby, it’s probably because the stakes were higher in Halo 3.
Short version - I agree with a lot of what you say and you are entitled to your opinion. Some of the issues do have an explanation but I hope some of the above offers you some insight to why some decisions were taken with Halo 3.
