I would like to throw my support over to a Ground secondary typing. Flying/Ground, first off, offers very interesting concepts, as it's never been done before. But that's immaterial. More importantly, Flying/Ground offers immunity to Electric and Ground attacks, two common enough types in the metagame that it is simple for CAP 1 to switch in on a target, take advantage of the immunity, and regain momentum. Flying/Ground also eliminates the Stealth Rock weakness - while as the OP said, an SR weakness isn't the end of the world, it is still a substantial factor. A downside, as mentioned before, is a 4x Ice weakness.
However, remember to take into account the theme of momentum - the fact that a Flying/Ground CAP will have a strong counter in Ice attacks makes it much easier to predict what move and what switch-in the enemy will choose, allowing you to switch out accordingly. This fits well with the theme of "momentum".
The second best choice would be Flying/Poison, simply because of amazing typing (the 4x fighting resist in particular). I would like to note, however, that Flying/Poison offers less offensively than Flying/Ground does - Poison STAB fails to be useful against most targets, to be quite honest - very few threats actually have need to be scared of Poison STAB, among these Virizion and Breloom, both of which are countered by Aerial Ace/Brave Bird/whatever Flying STAB we give CAP 1. Flying/Ground, on the other hand, gives us a potential EQ/Brave Bird combo or something similar; a type combo which hits 8/17 types in the game for super effective damage and isn't resisted by any one type.
In addition, Flying is resisted only by Electric, Rock, and Steel, all three of which are hit super-effectively by Ground. Ground is resisted only by Bug and Grass, both of which are hit super-effectively by Flying. Flying/Poison, on the other hand, is walled by all three flying resists, Steels in particular. With Flying/Ground, the only thing to worry about is enemy Flying types, which makes the only viable resistances to Flying/Ground dual-typed Flying pokemon with a secondary typing of Electric, Rock, or Steel.
Do note that this includes a good amount of Pokemon in the game, however, some of the most prominent being Zapdos, Aerodactyl, and Skarmory - probably more in the 5th gen too, but I'm not as familiar with them yet as I'd like to be. Note also that Balloon usage could be a potential problem.
Summary: I suggest, as many others have as well, Ground or Poison as the secondary typing.
Strong points of Flying/Ground: Resisted only by Flying/XXXXX, where the secondary typing is Electric, Rock, or Steel, or when an enemy Pokemon that has a Flying resist is using a Balloon, like Heatran.
However, remember to take into account the theme of momentum - the fact that a Flying/Ground CAP will have a strong counter in Ice attacks makes it much easier to predict what move and what switch-in the enemy will choose, allowing you to switch out accordingly. This fits well with the theme of "momentum".
The second best choice would be Flying/Poison, simply because of amazing typing (the 4x fighting resist in particular). I would like to note, however, that Flying/Poison offers less offensively than Flying/Ground does - Poison STAB fails to be useful against most targets, to be quite honest - very few threats actually have need to be scared of Poison STAB, among these Virizion and Breloom, both of which are countered by Aerial Ace/Brave Bird/whatever Flying STAB we give CAP 1. Flying/Ground, on the other hand, gives us a potential EQ/Brave Bird combo or something similar; a type combo which hits 8/17 types in the game for super effective damage and isn't resisted by any one type.
In addition, Flying is resisted only by Electric, Rock, and Steel, all three of which are hit super-effectively by Ground. Ground is resisted only by Bug and Grass, both of which are hit super-effectively by Flying. Flying/Poison, on the other hand, is walled by all three flying resists, Steels in particular. With Flying/Ground, the only thing to worry about is enemy Flying types, which makes the only viable resistances to Flying/Ground dual-typed Flying pokemon with a secondary typing of Electric, Rock, or Steel.
Do note that this includes a good amount of Pokemon in the game, however, some of the most prominent being Zapdos, Aerodactyl, and Skarmory - probably more in the 5th gen too, but I'm not as familiar with them yet as I'd like to be. Note also that Balloon usage could be a potential problem.
Summary: I suggest, as many others have as well, Ground or Poison as the secondary typing.
Strong points of Flying/Ground: Resisted only by Flying/XXXXX, where the secondary typing is Electric, Rock, or Steel, or when an enemy Pokemon that has a Flying resist is using a Balloon, like Heatran.
