Rafael - it's a bit of a circular debate and a 'chicken or egg' situation. Some established journals may have 'lost their governance' because they 'rest on their traditional laurels'. Some newly-emerging journals may have set up good governance structures - but cannot claim credibility because they are not established yet. For those, in-between, governance is maintained through recruiting effective editors, editorial boards, support administration - and maintaining an effective reviewer database. That, in itself, is tricky enough to maintain - never mind improving the governance. If I had to make a call though - I would say that improving governance is linked to how effective the Editor-in-Chief is - and how well they work within the remit and business model of the senior publishing team. I've been involved with very established journals that have 'slid dramatically' down the IF scales etc once an effective senior editor moves on and is replaced - only for the next editor to soon move on themselves - then it becomes a bit of a 'slippery slope'.
Peer review, citation index, network analysis... all singular pieces of a very large puzzle aptly called 'research measurement'. There's a recent book which may give adequate answers ... or pose more (intelligent) questions for ... future research (of some quality):