I imagine there was a realization during the drafting phase of this movie that went something like this: "Hey, remember how Christopher Nolan made Batman Begins and everyone thought it was great, but that the female lead didn't really work, and so in the sequel they had the hero's biggest nemesis kill her? We should do that."
The attempt to use Irene as a Catwoman-ish figure never really worked because the franchise ultimately kept true to Holmes' basically unromantic nature. And, really, the Holmes/Watson duo ultimately doesn't need a woman, though they've dutifully added another female character to keep the representation up and contribute a bit to the plot, though without any romantic overtones. Noomi Rapace doesn't do a whole lot, but she looks striking (very distinctive face, especially the eyes). Actually, Mary (Kelly Reilly) shows some promise that respect.
This is the Holmes and Watson show, of course, and the routine is as much fun the second time around as it was the first, which is nice. Jared Harris is a very good Moriarty.