Well, I've been playing Aftermath for a couple days now, so I can make some comparisons between SS & AM.
There are a number of good features of SS which I like. Obviously, the first is the pseudo-destructible terrain. Can't beat the feeling of collapsing a building on an enemy and killing him without him realizing what's happening before it's too late. Secondly, you can fight in multiple levels in Silent Storm. Wanna get on top of a roof for a sniping position and an overview of the surroundings? No problem. Hear someone moving around upstairs? Toss a grenade through a window. Buildings are nothing more than eye candy in AM. Character specialization in SS is much more robust and improvement is immediate. You gotta wait in AM until you get to the next level to allocate improvement points. Silent Storm has a fully-implemented melee structure. You can stab enemies with knives, toss throwing stars, bludgeon a baddie over his head with a billy club or even duke it out with your fists. It's all there and it's a wonderful touch.
The things which AM has going for it are pretty good as well. There's of course the research element. It's a little lack luster in AM. Although, I don't miss this aspect much in SS either. The graphics in AM are on par or even a little bit better than SS I think. The maps also seem to be bigger too which is nice. Medics and injuries are much better in AM. If you can't patch a guy up on the field and he comes back to base injured, he'll be spending some time in sick bay recuperating. This element is poorly constructed in SS and downright unrealistic as well. Instead of a "core" group of 20 agents and a max of 6 on a mission like SS, AM opted for a max of 7 but with an unlimited pool of randomly generated recruits to keep as time goes on. I just wish you could have a bigger pool to draw upon initially instead of running missions short-staffed.
There are a bunch of other things which I'm forgetting right now, but the race is neck-in-neck. If I had to pick one right now it would be Silent Storm. That's simply because there aren't as many annoying features in that game.