Remember, that the main reason why all weapons should be able to hit through wings is that the elemental with wings has to descend to attack another elemental, so the other elemental should be able to retaliate with any weapon he is holding.
As for Marvaddin's points:
1. Fog Shield + Wings at the same time would be too powerful. Fog Shield is quite good in itself and it would give you enough time to play Wings, then you'd receive almost no damage, unless your opponent has mostly airborn creatures, but then you don't play wings.
2. As it is right now is good enough. Flying does look like a passive ability to me, while having a number of passive abilities (or faking it with a separate ability for each combination) solves the problem.
3. That's the change I'd like to see. In fact weapons do deal a lot of damage when compared to creatures. Some decks, can kill with only a weapon (Fahrenheit, Titan, Morning Glory, Arsenic, Vampire Dagger, Eagle Eye are great for that, but even Poseidon denial works). The fact that weapons avoid a number of shields already (eg. procrastination, gravity shield, cannot be frozen by permafrost) already makes them better at dealing damage than dragons in many cases.