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'To have a full agenda' = to have lots of issues/problems to sort out/discuss/deal with. Meaning: 'The Union had plenty of issues to sort out, including its relations with Belarus and the WNIS [Western newly-independent states]. However, these were overshadowed by the EU's ....' ('On ....'s full agenda' followed by 'however' is an unfortunate construction to use here, as 'on' can often mean 'on the subject of'. As a result the sentence appears at first sight to be a clumsy joining-together of two separate sentences. It's only when you read the paragraph a second or third time that you start to understand it).
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