I've never ridden an atlantis, older or newer, But I do ride a '21 joe appaloosa(60) (the joe is very similar to MIT atlantis) and a rambouillet(62/63), so I feel I can comment a little on long vs. short chainstays.
In addition to taking the joe out on road and gravel, i treat it as my mountain bike. I've ridden a fair bit of twisty singletrack in NC and have never really felt inhibited by the long chainstays. Anytime theres a turn I can't make, I honestly wouldn't be able to do it on a shorter bike either.
Also, I recently did a little test ride with a new packing setup and I felt it really demonstrated the magic of the long stays... rear rack and panniers. Just honestly blown away by how roomy the bike is and how out of the way the luggage is with the long rear end, and how little it affected the good handling of the bike. I'm typically a front basket guy, but these bikes do ride really nicely with the weight in the back. On other bikes I've had issue with my heels hitting the bags.
Now the Ram with the more traditional geometry is also a fantastic riding bike. I'm not sure how the geometry compares to older atlantis', but the rear end is considerably shorter than the joe and MIT atlantis'. I currently run 700x38 panaracers on it and use it for paved and dirt roads. Obviously not as stable as the Joe on gravel, but its really a road bike and it kicks butt on pavement. I'd say I like the shorter rear end for pure road riding. If it were sturdier I could imagine putting bags on it for a tour, but it wouldn't be as spacious as the setup on the Joe.
As others have stated, the older and newer atlantis' are really quite different bikes, and in choosing between options you just need to analyze what features you want. The newer models can fit bigger tires, are roomier, more stable, but come at the cost of being humungo bikes. For me personally, I like the extra tire clearance and I like having at least one long chainstay bike. These days its a bit of a key rivendell feature. I feel lucky to have both options in the stable.
Also if its possible, the best thing to help in deciding is getting to try each style out to see what suits you. Maybe there is someone living close enough to you with a long chainstay bike you can try, or an older atlantis. worth checking the riv map John created or asking the group.