First off, ass a prequel, it totally destroys the storyline, that is correct. However, not all the flaws mentioned necessarily conflict with known facts. to start, the invasion of Reach is portrayed differently in the book and the game because they are through the eyes of different people and in different places. Hence, grander, global contradictions may not be the case the Covenant or UNSC may have employed different strategies in different areas, or there could have been communications errors, etc.
Secondly, only Jun survives the game by escorting Dr Halsey to CASTLE base at the end of the game. And, the Spartans IIs in The Fall of Reach arrive to find her alone. It is not entirely inconceivable that Jun may have died during the transition, or that he died inside CASTLE base and the Spartans IIs simply never found his body. He could also have left after completing his objective or any number of things.
One of the things that Greyfox105 mentioned is that the Spartan IIIs were not wearing the SPI Armour described in Ghosts of Onyx. This is explained in that Noble team was equipped with extra equipment and better gear to better suit their specific objectives. However, what IS of concern is where the Spartans came from. Take the player for example. He (or she in my case)is listed as B312, the B indicating that he is a member of Beta Company. However, 298 of the 300 Spartans in Beta were killed in OPERATION: TORPEDO. The books and games talk of at least four Spartans of Beta who were removed before the battle of Pegasi Delta, but The Ghosts of Onyx clearly states that there were only 300 Spartans of beta company selected for augmentation and only two survived. These were confirmed to be Lucy-B091 and Tom-B292.
The main issue is in fact, how Dr Halsey knows the Spartan IIIs. in Ghosts of Onyx she meets a Spartan III for the first time on Onyx. Yet, in SWORD base, she seems totally familiar with Carter and the rest of Noble Team. She is friendly to Jorge because he is a Spartan II, yet all the others, who are Spartan IIIs, were not known to exist by Halsey at this point.
I could wax on about other plot holes, such as why Cortana needed to get to the Pillar of Autumn is never explained. Also, Halo: Reach makes the emotional response Cortana has in leaving the Autumn rather stupid, as she had literally just arrived on board. But the main points are there. The game has a good compelling story, but it requires you to ignore the rest of the Halo universe (Something easy for a lot of people i'm sure) and the characters are very one dimensional and shallow.
I would also like to point out that as Space Spoons iterated, the Spartans were expected to work cooperatively, (no pun intended) instead of hierarchically. Although Carter would always have the final say on an issue, he would be remiss not to encourage and listen to the suggestions of his team members.
Lastly, to Eclectic Dreck, the Spartan IIIs were not actually soldiers before training, they were young children just like the Spartan II class. The only difference between II and III is that the IIIs were specifically selected from orphans or refugees who had a reason to hate the Covenant. They also accepted less stringent genetic profiles for training.
