This was my first thought when I started reading this thread. When you have two different print magazines, it makes sense to focus each on a target audience. But subscribers automatically get all the articles, so why the arbitrary split?
What I would prefer to see is articles classified according to type: adventure, side trek, bestiary, campaign, class, etc. Subscribers should be able to look for articles within those categories.
Even better (I don't know if this technology exists, but it should) imagine being able to select several articles and having the system create a single PDF file with only those articles. No more searching through several issues to find a particular article, or for each article in a series. I'm not a subscriber, but I assume each article can already be downloaded as a PDF (if not, why the heck not??) so I would think combining them into one file would be possible.
Moving online is more than just eliminating the use of paper for printing - there are so many more options available, both for WOTC and their DDI customers. Why not use them?