I have a rune page with armor yellows for when I know I am running against an AD mid. With solo Q you never know what you will face.
For example yesterday I faced a Talon mid as Veigar and I ran armor yellows. I was able to out-trade him and get an early game advantage. ( of course I underestimated his lvl 6 burst and we ended up being pretty even throughout most of the game :) )
For rune pages in general it really does depend on the champ so I would take any answer here with a grain of salt.
But in general I think that flat mana regen is almost always better than mana regen per level. This is because mana regen for most AP champs is most difficult in the first 6 levels. By the time you get to the point where per level runes are better you should have blue buff and potentially have items that compensate. In the first 6 levels you want enough mana to harass and out-damage your opponent.
The other thing to consider is potentially going flat magic resist blues in order to out-harass your opponent (of course only if you are facing an AP champ). An early game CS advantage is extremely important so that magic resistance can really make a difference. And just as above with mana regen, flat is a good choice to get the upper hand in the first 6 levels.
For quints movement speed is often the best choice on many ap-mid champs. This is especially true when facing an opponent with skill shots (Karthus, Morgana, Anivia, etc). More movement makes it easier to dodge those skill shots which can be the difference between winning and losing the lane. Movement speed quints will sometimes make you faster than the enemy jungler making it easier to escape ganks.
I wouldn't worry too much about the enemy team composition when considering runes. It is most important to pick a rune page based on your lane match-up.