I used D2D for MI1:SE and Steam for MI2:SE (only because Steam was the first to sell MI2 and I needed it FAST).
I haven't had any big problems with either version so I don't think it's a big deal which one you take. Since I have no real interest in most of Steam's features (like chatting with friends, achievements) I do prefer D2D for it's simplicity.
You don't need to install any extra software to play the game (they offer some sort of program for downloading but you don't need to use it). When you've downloaded the installer it's just an .exe file that you can easily backup.
I can't remember activation too clearly, but I think you might need to be online the first time you launch the game. I'm not sure about this though. Also every time you install the game you need to enter your product key. But I can definitely say that once you've activated the game it doesn't matter whether or not you're online.
One thing that annoys me about Steam is that after I've played my game, Steam still runs on my system and I have to manually close it from my taskbar. Maybe there's a setting to turn that off. But with D2D, nothing else appears to be running... just the game while I'm playing it.
Steam has several great features in addition to the game, whereas with D2D you basically just get the game. So if those features seem appealing to you then I'd recommend Steam. But if you just want to keep it simple. D2D is the way to go.