Bareboat means you take the boat and skipper it yourself. Skippered means somebody else handles it. The choice is usually made on price, which is the wrong reason.
What operators will ask you
Requirements differ between operators, and they differ more than people expect. Some will want a recognised certificate; some will want to know where you have sailed and in what. Ask before you book rather than at handover, because a disagreement on the pontoon on the morning of your charter is a ruined week.
The argument for a skipper
A skipper knows where it is worth going on the day. In Malta that matters more than it sounds — the wind decides whether Comino is calm or unusable, and somebody who sails these channels weekly will know before you leave the marina.