AC3 did actually have more bits with Desmond Miles, aka the most boring Nolan North character ever. There were even combat sections and I distinctly remember an underwhelming chase sequence where you kill the bearded Templar scientist who was the main villain of the modern day plotline in the Altair and Ezio games.

The female lead didn't die in AC2, but the next game, AC Brotherhood. I seem to recall hearing somewhere that the actress playing her was contracted for 3 games and intended to have a pivotal role in the originally envisioned trilogy, but then AC2 was a huge hit so Ubisoft turned Assassin's Creed into a yearly franchise, starting with the two Ezio spinoffs in between 2 and 3. Her contract was up so they just killed the character off in a filler episode