Hit Shepard with an omnitool... by that you mean she impaled his chest with a enormous omnitool blade, the very type Shepard can use to finish off Kai Leng. Frankly if that didn't kill him I'd be surprised.
Legion is a machine, its little surprise it can hold up Shepard. Saren was able to left up and choke Shepard one-handed aswell. The real crime in this scene is that Legion, a machine, gets taken out by a little dagger in the backplate.
If you consider these two instances to be "wimpy" (one of which was in ME1 in regards to Legion's throat-grip) then I don't know what to tell you. Just how much testosterone do you need for something to be manly and fierce? Even Wrex, the walking testosterone tank, is a wimp in the cutscenes if you turn on him. Wrex and Legion's weakness stand out a lot more to me than Shepard dying frorm a giant blade impaling his chest or being lifted by a geth.
Oh, btw? That wimp survived Harbinger's laser blast, getting shot, bleeding out, having the citadel explode around him and get crushed by rubble. What a pansy!