The alliances on the alignment wheel are represented to some degree in 6th ed. 40K and, generally speaking, the wheel is well-arranged. However, there are still some issues with the alignment wheel from both a thematic perspective and a game-mechanics/design perspective: 1) It doesn't represent degrees of allegiance like the 40K allies matrix, so hypothetically you could end up in a meta where you see lots of DE/Chaos decks and, as they are classified as "desperate allies," this should really be reserved for corner case scenarios. 2) There are alliances that are not represented on the alignment wheel such as Tau/Orks and Space Marines/Eldar who are allies of convenience. Yet DE/Chaos make the cut? 3) The 6th ed. 40K allies matrix may be in line with the latest GW fluff, but a lot of us 40K players view it as a marketing scheme to get people to buy out of faction miniatures. I prefer my 40K with more paranoia and xenophobia. Factions that are battle brothers are OK occasionally and these and other alliances such as those mentioned above could be enabled by specific cards in Conquest. This last point is obviously more a matter of taste than an objective comparison between the alignment wheel and the allies matrix. In the grim darkness of the far future, I'd like to see less friendship.
I realize that the alignment wheel will almost certainly remain in place if for no other reason than that the core set must include enough cards to construct playable 50 card decks. While this is an advantage for the core set, it may become a liability for the long-term health of the game. Combined, the pitfalls of the alignment wheel listed above could potentially lead to issues with deck diversity and corner case alliances that are now somehow commonplace.
To offer one hypothetical, if Orks and IG prove to be highly synergistic, then suddenly you'd find yourself playing against lots of competitive Ork/Guard decks. I don't mind this combination sometimes (Blood Axes, mercenaries) but it would be a shame if all competitive Guard decks included Ork allies. That's just one hypothetical example but we all know that when decks are optimized for competitive card games, you tend to see similar archetypes over and over. The stultification of deck lists is both common and unfortunate in card games; look at Sith control in Star Wars where two or three objective sets have been dominate since release. It's even worse when it's some strange combination that may not be entirely unthematic but still shouldn't be commonplace (e.g. Orks/IG or DE/Chaos).
The easiest way to address these issues is to do away with the alignment wheel altogether and embrace the distrust and xenophobia of pre-6th ed. 40K. Occasional alliances could be made possible through card text.
If alliances are to play a large role in the game, I think the alignment wheel could at least be more flexible. A more elegant design solution would be to indicate potential ally factions on the warlord cards, e.g. a Blood Axe warlord could ally with Imperial Guard, whereas a Gahzghkull warlord card would not allow guard allies. This would also provide a design mechanism through which we could see other ally possibilities such as Chaos with corrupt Guard, Orks manipulated by Eldar, etc.
This hypothetical change would not require re-balancing individual cards or an overhaul of the core rules. In practice, all that would be required is that warlord cards display the icon of the faction(s) with which they may ally and a number that indicates how many cards from other factions that hero's deck may include.
If allies were specified on the warlord cards, it would even be possible to adjust the degree to which a particular warlord might be willing to accept allies. That is to say, a one warlord might be willing to accept 10 allied cards in the deck whereas another warlord might accept only 5. Abandoning the rigidity of the alignment wheel also opens up more interesting combinations such as a radical Inquisitor warlord that would allow for some daemon cards to be included in the deck, or a less xenophobic IG commander to take Tau allies. In cases where alliances might create powerful synergies, balance can be maintained by simply restricting the number of ally cards permitted. This just seems like a more flexible and modular system that would allow for more thematic, diverse, and customizable decks.
There are plenty of ways this might be addressed and this is just one possible suggestion. I'd just like to see groundwork in place for a highly thematic and diverse meta for this promising game.
EDIT: Added introductory paragraph and clarified incorrect terminology