I haven't finished this yet (playing very thoroughly), but here are some more observations:
The hub worlds are awesome, much larger than in DX1 and containing tons of stuff to do. They aren't linear like the other maps and encourage you to just go around and explore everywhere, an aspect sorely missing from most modern FPSs. It's a pity that there are only two of them.
Like the first game, the augmentations are not very well balanced. Some are obviously more useful than others, and quite a few seem rather pointless regardless of your style of play (like the hacking analyze or jump silently ones). This is an issue with some weapons as well, with the pistol somewhat overpowered (especially with a silencer) and the sniper rifle relatively gimped. The sniper and combat rifle also have some annoying bugs with certain upgrades. I would have preferred to have the skills from DX1, but the weapon mods do still force you to choose certain weapons to invest in.
Money is much easier to come by than in DX1. You get small credit cards all over the place and can quickly rack up huge amounts by selling guns. If there are several identical guns lying around after a fight and a seller is nearby, you can sell each one. I have something like $40000 and have stopped collecting them now.
As for that boss people were talking about earlier, I blew him up with a rocket launcher and won easily that way. The launcher takes up a ton of space and is not worth carrying around permanently, but you can get one earlier in that same level.