In addition to being an extremely well-crafted series in terms of playability, Halo contains one of the richest, most deeply thought-out and exploration-worthy universes in a video game. Its density of fascinating ideas and locations rivals that of established novel series like Iain Banks' Culture or Alastair Reynolds' Revelation Space. Greg Bear's Forerunner Saga books land among my favorites of the past several years, and though I have only recently become invested in the main series of Halo books, I find them by and large to be a rollicking good time, if occasionally simplistic. Just existing in the world of the first game consumed days of my time.
However, that world is compromised, to my mind, by two plot points: The kidnapping of the original SPARTANs and their scarcity during the events of Halo:Reach and beyond. Now, before beginning, I should say that my investigation into this issue was triggered in part by a negative emotional reaction to the Halo 4 launch trailer and the series' general heroic portrayal of the kidnapping and torture of children. I will attempt to include only my rational arguments against these specific aspects of the story in this article. I believe they will be more than sufficient.
The kidnapping of children and their subsequent transportation across the galaxy is an incoherent notion. The price of FTL travel, while evidently not beyond the means of a secret government project, cannot be small, running counter to the idea that the SPARTAN program suffered budgetary constraints. Instead of implementing a bizarre and complex clone-kidnap-transport plan, a more cost-effective method would be to alter the DNA of embryos to suit the program perfectly. Given that this society is able to alter an existing person's DNA, it seems unlikely that they would be unable to do so in an embryo, or that it would be easier not to. Even in the event that such technology has not been developed in the intervening 500 years, they could still use the seemingly comprehensive genetic database of UNSC citizens to select optimal pairings among people on and near Reach, mitigating that cost. Additionally, there are currently techniques which can successfully convert skin cells into both eggs and sperm, even from juveniles who may be incapable of donating them. If samples were taken from the original subjects, combined and incubated during the early days of their training, the resulting SPARTANs would easily have been able to participate in almost every battle of the Covenant War. Many could be created, and only those best suited kept. Keep in mind, such techniques would be as old to them as movable type is to us. Given the early success of the program, its cost, the no doubt pitifully tiny investment necessary for in-vitro fertilization and exo-womb/surrogacy, and the enormous number of inferior SPARTAN-III soldiers produced, there is little reason not to produce enough at least to account for attrition during training.
Scrutinization of Bungie's official timeline shows that the SPARTAN project began and Master Chief was kidnapped before first contact with the Covenant, and before the development of the MJOLNIR armor. In addition to casting the UNSC in a dubious moral light, this dispels the notion that there wasn't enough time to create new, perfect children before the invading forces caused irreparable damage to UNSC holdings. They were developed to combat relatively small planetary rebellions, a mandate which would hardly require haste, much less the addition of uncontrolled variables to a secret experimental military project. The six years necessary to reach training age would not be seen as critical absent fore-knowledge of the coming war. All these coincidences just happen to align to put Master Chief at the front lines exactly when the Covenant arrive.
Even if the program was stretching the limits of its funding by the time its fruits saw combat, the SPARTANs entered service and demonstrated their usefulness almost 30 years prior to the events of the main Halo series, and the SPARTAN-III project was embarked upon more than 20 years before the events of Halo 3. Time was not an issue. Given the training and willy-nilly sacrifice of one hundred thousand SPARTAN-IIIs, cost also seems not to be an issue at that point. Even if the SPARTAN-II technique were massively more expensive, the drastic reduction in casualty rate and increased performance make them a more sound investment, demonstrated by the events of Halo: Reach. A situation could be imagined where Halsey's funding were co-opted by supporters of the angry orphan model of SPARTAN-III, but that is not alluded to in any source material, to my knowledge. Rather, the small number of SPARTANs, like their origin story, is contrived in order to provide Master Chief with a heroic mystique, without any regard for realism or logic.
Some may call all of this sacrificing unimportant details for the sake of better storytelling, and I agree that such sacrifices are often positive if in the service of making a story more interesting. However, in the case of Halo, I find it to be a deep compromise of the beautifully crafted universe in the service of an emotionally manipulative cliché.
Cetainly, the novels rebut some of these points to some degree or another, slouching their way to technical marginal internal consistency. And if Halo took place in a different universe, one where all my points are differences between our world and theirs, it would be less of an issue (while still beggaring belief). However, Halo exists in our own universe, including a future version of our own Earth or one indistinguishable from it. Even if there were a catastrophe which annihilated all extant technology between now and then (which the Halo timeline does not include), the idea that they could re-develop DNA alteration but not have cheap, advanced in-vitro fertilization is frankly ludicrous.
In good non-allegorical fiction, the plot arises from a coherent world or exists within one; Identification with characters arises from their depth and growth. In the case of the Halo series, a heroic plotline was chosen and the world haphazardly altered to suit it in a (successful) bid to manufacture mass appeal. This amounts to the slothful unwillingness to apply any but the minimum level of effort in crafting their protagonist. There are other issues, such as the inconsistencies with the historical Spartans' training and the implied retcon of the timeline to bring the Covenant's attack earlier, but none take me out of the story as much as these two. And that's the real crime, not the plot holes themselves. I can certainly understand Bungie's inability to apply any significant characterization to a faceless space marine. Heck, they didn't even try in the first game. However, with the addition of the various novels, comics and web series, there is little excuse for this level of laziness in a world which is obviously the result of Herculean effort and a huge amount of talent.