They did a clever thing with mechancs and hit points. You heal by taking cover. Combine this with more aggressive enemies, thus making want to take cover ASAP, and you wind up with gunfights that feel far more like gunfights. There a distinct brutality in these fights. They're more edgy.
I thoroughly understand why the fighting mechanics. In ME1, you went on a random fight, opened the door, kicked the hornet's nest, and hoped that you withstood the onslaught. That's pretty boring and repetitive. It feels video-gamey. The fights for ME2 feel less video-gamey and feel more immersive. This is clearly their intent. They obviously spent a long time on the feel and polish of the fights.
The fights themselves are more than static encounters now. Some are just skirmishes, but many of these new fights are multi-layered. They inherently stand against a "stand still and fight" strategy. The dynamics push you into dynamics. In last night's fight against a "tank", you had to make it to the tank while foot troops slowed you down, allowing the tank to fire. Cool dynamic. That's another thing that they do. They change one of the rules in a very physical way, such as waves of opponents, an opponent in a strategically good position, environmental hazards, and so on. All in all, the design work felt far more interesting.
Different weapons now feel different. In ME1, they just had different stats. Now, those weapons have different behaviors. A grenade launcher acts different from a missile launcher, acts different from a particle beam.
Ammo puts limits on the usefulness of weapons. I would go in and sniper all day long, but I run out of ammo during many fights, and I need that ammo for the tougher fights. So, you can't even rest on your favorite weapon in a long fight. These "natural" limitations do make the game more interesting.
There's now a whole mini-game in research and development. You explore planets for resources, then you use those resources to build yourself more stuff. It makes exploration more engaging.
All in all, the design team took all its lessons to heart and innovated pretty well.
For leveling up, this is the first game ever where I just choose "auto level up" for my character. I just don't think that the choices matter enough. In general, because of the escalation of costs, cranking up one score just becomes prohibitively expensive. With just five skills, you use those skills all the time.