The "nearly powerless" refers to blocking the bill being the only thing the parliament is able to do. The commission can just keep proposing this bill, it only needs to pass the parliament once. Once passed, future parliaments are unable to amend or repeal the bill. The commission only has to win once, while the parliament has to block the bill every single time.
The commission isn't an extraneous entity, if the parliament and member states want a law or amendment the commission will write a proposal. It doesn't "have to" strictly speaking but it would.
Framing it like you do is ignoring the fact that the only reason we're here in the first place is because a good chunk of member states and MEPs want this law
