The second has a better system for the use of talents/guns against defenses. That's not to say the weapon and armor mods from the first aren't fun though. The outcome of the two systems is more or less the same, reaching that outcome is very different though.
In the first you the had Armor-Piecing/Tungsten rounds mod( That dealt more damage to synthetic enemies ) that you would equip on each individual gun( for you and/or your squadmates ). You find better versions of this ammo as you progress, so you could have level 7 of, your cronies could have levels 5 or 6 or even 7 if you have a few to spare, etc.
In the second, only one of the characters you recruit has the ability and leveling up that ability increases its effectiveness. Eventually when it reaches max level you can choose to have it effect the entire squad( everyone gets armor piercing ) or just him with greater effect.
So ultimately, you can spec out how you and your squad get armor piercing, but the way you get there is a bit different.
The first has a much better overarching story. The second pretty much doesn't have an overarching story and lacks the big bad villain; It's all about the characters you're bringing onto your crew and their stories. The second weighs heavily on how you like those characters. I didn't care for some of them, dealing with their personal issues when I'd rather be part of a space opera and dealing with larger issues.
Even though some of the characters in the second were hit and miss for me, I always enjoyed the combat. Definitely play the first though, I found the main story missions much more interesting than the second's.