I'd like to have Cable on my side too. Yeah, currently his powers are gone, but with the gravimetric and dominus tech, he basically replaced them. With the gravimetric sheathe he has force fields and can create objects somewhat like Green Lantern. With the dominus stuff he can access a worldwide infonet and mimic telepathy to some extent. Plus with Providence (and perhaps Rumekistan soon) at his disposal, he's one tough opponent.
As far as Cable and Deadpool being more about Deadpool, I think it's been fairly even overall. Some arcs focus more on Cable, others on Deadpool, but they hinge on both of them being there. Currently Cable just overthrew a European government and took control, he's not just sitting in the background.
As to why Bullseye is attacking Peter, he's an assassin for hire, probably Kingpin or someone sent him after Spider-Man.