Usually in systems where you need A and B to agree to pass a legislation, if A start blocking B's initiatives, B starts blocking A's initiatives in response. If the Council and the Commission always go against the Parliament's will, I expect the Parliament to block their initiatives in return, causing a permanent state of gridlock, until some truce can be reached. If this does not happen in reality, why doesn't it?

it's a multi-party system (dozens of parties)

you can create a majority somehow most of the time