It is different, but it works out so far.
Although there are fewer weapon choices to make, you do still get to upgrade weapons as you go. One of the other new large parts of the game is a research system. As you collect minerals (from both unexplored planets and from caches during missions), you can use them to research new upgrades. You can research upgrades for particular weapons (and buy a couple of the upgrades outright from the shop). These upgrades affect an entire item category, like +10% damage to Sniper Rifles. While an increase in damage is the simplest type, it is not the only type. As you unlock enough boosts, you'll get more advanced research, like an increase in armor penetration or an increase to headshot damage while using Sniper Rifles.
You can also research upgrades to unlock new heavy weapons, or to increase particular characters attributes (for example, there is a research to upgrade the Tech Damage of a particular character by 10%).
And, not to be forgotten, you can upgrade the Normandy's systems. As you are searching to fight a more technologically adept foe, your ship needs some enhancement as well. You will need to upgrade the ship's armor, weapons, and shields to have a better chance of survival. Other ship upgrades offer more directly useful enhancements, such as cutting the time it takes to search out new minerals and missions on planets, or increasing fuel you can carry, which will increase the distance you can travel from refueling bases on the galaxy map (and, thus, the planets you can visit).
Oh, and Moon Rabbits, the Mako is gone. There is a drop ship which will drop you at points to start ground missions on unexplored planets, but the exploration and fighting is done on foot. Although according to the wiki, there is a Hover Tank availible for DLC, I have not yet encountered it (I haven't done the DLC missions yet). But it is not required.
