So we have all had a chance now to play some 40k under sixth edition. I have found fliers to be quite formidable and I will add flying monstrous creatures (FMCs) to the list below since they function in a similar manner. Some armies have access to fliers while others don't but via allies most every army can take at least one. There are two ways to go about designing a competitive army now - you can adopt either an offensive or defensive stance in regards to fliers when building an army for 40k6 now. Let's take a quick look at the armies that have access to fliers or FMCs:
Blood Angels - Stormraven
Chaos Daemons - Bloodthirster, Fateweaver, Lord of Change & Daemon Princes
Dark Eldar - Nightwing (?) & Voidraven
Imperial Guard - Valkyrie & Vendetta
Grey Knights - Stormraven
Orks - Dakkajet & two others (sorry they slip my mind and I have no experience with or against them)
Space Marines - Storm Talon
Tyranids - Harpies, Parasite of Morthrax & Hive Tyrant
The Stormraven, Valkyrie and Vendetta have the highest armor (AV12) but weigh in at a premium for points compared to other fliers. Two Stormravens in one army are a considerable amount of points while the Vendetta is more affordable and offers better anti-flier capabilities in my opinion with three lascannons. Necrons seemed to have transitioned quite well from fifth to sixth edition and I rate the Doomscythe as the best overall flier which bares tangible evidence from the first 6th edition GT (Golden Throne) held earlier this month in San Jose, California. The Chaos Daemon flying circus is also another formidable list that can field up to five FMCs. Chaos FMCs are quite resilient in the swooping mode coupled with good invulnerable saves... If you don't have the right tools it can be a long day at the office so to speak. The rest of the bunch are kind of in between in my opinion.
I am currently of the mindset to go more defensive versus fliers and FMCs. We don't know when GW will release the flakk missile and if it's of limited application then the filer could be the new mech nemesis. To effectively deal with enemy fliers and FMCs I'm currently building my lists to incorporate high volume of firepower coupled with twin linked weapons plus the use of the Divination primaris psychic power. While fliers are certainly very strong coming out of the gate they all have some inherent weaknesses that can be exploited. I have found that while one Stormraven won't last long versus an enemy army with a high concentration of fliers it's still one of my best counters. The Grey Knight Stormraven armed with hurricane bolter sponsons and psybolt ammo can typically drop one enemy flier in one shooting phase. Even if you force an enemy flier to evade that is something as you have greatly shut down their firepower for the following turn and they might been be forced to fly off the table.
There are other good defenses such as the Aegis defense line with a quad gun - combined as such the two elements provide excellent cover while being able to potentially pick off an enemy flier in one shooting phase. The total points (100) for the pair is a great deal for any army.
We were told that mechanized armies are going away in the new meta but I see them as another good defense versus fliers and with killpoint missions becoming more scarce. I think this is another effective answer in terms of defense versus enemy fliers. Cheap transports are still a good investment in most armies. The longer it takes for the enemy to take a crack at your troops the better.
To me it seems like Tyranids again drew the short end of the stick with no access to allies and the Flying Tyrant is very expensive pointswise for what you get in terms of performance. I used a Fyrant in 40k5 primarily in a support role to my army but now they are better suited as a vanguard. I think that Tyranids still have some solid answers such as Hive Guard if you're willing to adapt to the new reference frame.
So even with the vast multitude of armies that can be fielded now due to allies I see a new meta emerging and the flier is a lynchpin. It is what it is. If you want to keep playing your old 40k5 armies that's fine but be prepared to deal with units that inherently have a big advantage versus armies that rely upon little else than luck to drop a multitude of enemy fliers. It's still quite early but I don't see fliers taking a big hit from the proverbial nerf bat any time soon.