This is an issue that has been present in my symbolism studies, but seems to not be an issue for my readings in practice. It does tend to confuse when I help with readings, as I use the less-common style.
Generally you will find the Swords to be Air and the Wands to be Fire**. This is relatively common throughout most decks whether RWS/GoldenDawn based or not. I can see the basis for the association in this method, and do not think that they were switched for discretion.
One of the theories on the RW deck and the specific symbolism used was that the cards were able to be used as flash-cards in the G.D. training. You can look closely at the symbols and you will find they are both simplistic and not hidden. This concurs with the idea of flash-cards and helping initiates associate certain symbols with the steps of initiation and other systems like numerology, Quabalah, and astrology. Because of the inclusion of the symbols that were so ingrained in the G.D., there is no reason to think that Waite would have swapped one of the associations. If that were the case it would be a very confusing teaching tool.
On the idea of the deck being constructed with Wands as Fire and Swords as Air, there is cohesion. Generally when we speak of a wand, we think of our desires, wants, creativity, and passions. When we think of passions and desires we correlate the spark of life, and hence fire. This is representative of the will to live, and the idea of the spark of life; and though it is an idea (creative thought = wand) it is also a spark of passion (passion = fire, life).
(Note to serious Quabalah (or Kabbalah) studiers: this is a loose correlation to the four worlds concept, and is solely intended to demonstrate that the G.D. and Waite systems are aligned with the suits/elements connections in the tarot. Yes, I am well aware that the Four Worlds of Quabalah are very much deeper than this superficial explaination)...
To quote a website that I randomly selected (because others have put this into words and I don't need to):
*1)...the Four Worlds in Kabbalah. In the First World, we first receive a Divine Spark or Idea. In the Second World, we Contemplate the Idea. In the Third World, we Formulate a Plan. Finally, in the Fourth World, we Take the Action Steps necessary to bring that Divine Spark all the way through our Tree of Life into physical manifestation
The first world (WANDS) correlates to Fire, passion, desire, beginning of life. If you think of fire, it is eager to consume, live thrive and change. Fire is the beginning of the journey.
The second world (CUPS) correlates to Water, and our emotions and feelings as we contemplate the world around us, how we will interact as we pursue our desires. Water isn't the issue here, but note that it brings forth the idea of currents, the ability to make changes (not the changes themselves), and the fluidity associated with emotions.
The Third world (SWORDS) connecting to AIR is about putting together a plan, the tools you need, and the knowledge associated with realizing your desires. The sword is obviously a tool for getting things done. Additionally, you see in many pips that there is a lot of playing, training, and learning associated with the swords, but not much in acquisition. The sword requires intellect to use, and intellect is almost always associated with air.
The fourth world (PENTACLES) connects to Earth, the physical and real manifestation; and making real the ambitions and ideas that have been worked on. In the fourth world one makes things, takes action, and produces concrete results of the work previous.
This all points to the correct correlations of the RWS and Golden Dawn based decks as having a serious basis for the connections of Fire to Wands and Air to Swords. It tends to lessen the idea that they were switched on purpose.
I will second post about the other method, I don't want to risk a pc crash at this point...
To be continued.
*1)
http://www.clair-ascension.com/kabbalah.html