...I am a big fan of mass effect, and it is difficult to compare the 2 because they are a quite different experience. But if you liked one you should definately try the other.
Yes very different types of games. Both are great but in their own way.
I've only played Mass Effect 2. Excellent story and characters. However, although you get some flexibility with the recruitment, loyalty and misc missions, it is extremely linear. In some ways that's good because the developers can anticipate paths and form alternate dialogs and reactions.
Fallout 3 (like Elder Scrolls) is different. It sets up a huge world that you basically explore and interact with in whatever way you chose. The Main Questline is kind of secondary or lower, at least it is to me. Whereas in Mass Effect 2 the main quest line is pretty much all there is.
To the specific question of armor and weapon customization, you can't really do that the way you can with Mass Effect 2. But there are a variety of weapons, armor, and other articles you can use.