Where do you live, e.g., nearest big city/state?
How often do you think you'll be travelling with the tandem via public transport?
Do you need an XL or are you borderline for a Large? It's worthwhile to note that there are two Large S&S tandems -- a Co-Motion Speedster & a Bushnell -- listed for sale here:
http://www.tandemmag.com/classified/
Without getting into your finances, it suffices to say that dropping $8k on a "recreational vehicle" can rock some people's world whereas others just swipe the card or write the check and smile. If you are in the latter category, I don't think you can go wrong with the Santana. While most other builders are not inclined to offer Al S&S tandems given the need to be somewhat more delicate in their handling and potential challenges/expense associated with repairs of any travel related frame dings, Santana seems to sell a few of them and I've not heard of any problems. As for the cases, their oversized super-case is slick, but I'm still not sure if it's easier to manage that the two standard size S&S cases.
We use a hardcase for our frame components & handlebars and put the wheels, boxed cranks, & seats w/posts attached in a softcase. Also, as MerlinXLight notes, given that S&S coupled tandems have only been on the market about 10 years, there have been a lot of folks travelling with uncoupled tandems for a long time.
Rather than going through all the pros & cons, here is a link to a search of the archives for threads where "S&S travel tandems" appear where you can leisurely peruse what's already been written, some in great detail and with links to other resources:
http://www.bikeforums.net/search.php?searchid=1844040
Finally, and this gets back to my first question, while I don't think you can go wrong with a Santana Stow-away, given the amount of money you're about to invest in your tandem it may be well worth your time to visit a tandem speciality dealer who sells Co-Motion tandems, perhaps Bilenky or one of the other builder's who offer S&S tandems just so you can have something to compare the Santana and your Burley experience to. Each of these builders uses their own philosphy regarding materials, geometry, and fit and you might be surprised to find that the frame material can be least important thing in your decision process. Then again, it makes the decision process a bit more complex which brings us back to the economic factor: you can always buy the Santana and ride it until you decide you'd like to try something else.