Most of those resulted in “the laws in place are already good enough” responses. From your links

The EU response to stop vivisection:

The Commission considers that the Directive on the protection of animals used for scientific purposes (Directive 2010/63/EU), which the Initiative seeks to repeal, is the right legislation to achieve the underlying objectives of the Initiative. It sets full replacement of animals as its ultimate goal as soon as it is scientifically possibly, and provides a legally binding stepwise approach as non-animal alternatives become available. Therefore, no repeal of that legislation was proposed

The EU response to Save the Bees:

In its reply, the Commission underlined that rather than proposing new legislative acts, the priority is to ensure that the proposals currently being negotiated by the co-legislators are timely adopted and then implemented, together with an effective implementation of the CAP.

The EU response to Stop Finning:

the Commission commits to better enforce the EU’s already strong traceability measures by strengthening the enforcement of EU law that applies to the entire value chain - control of fishing at sea, full traceability of shark products from landing to consumer, consumer information, and prevention and redress of illegal trade - and ensuring the collection and reporting of complete and reliable information by fishermen and Member States’ authorities on all these aspects.