Hi. You've got good ideas on everything except Margarita Island I see, so I'll chiime in on that one. Most excursions at his port of call involve a long bus ride. The port itself is merely an industrial shipping area from which a tiny shopping area has been carved. It's an easy walk from the ship to the fresh air vendors, a wee shop selling alcohol, ciggies, and coffee, an outdoor cafe with a limited menu, and a sort-of beach where you can get a seaside massage, and some excellent wading in, but not good for swimming, snorkeling, or surfing. If you like "the long bus ride" you might want to take an excursion--otherwise, this might be a port where you choose not to spend your excursion dollars.
In general, here are my "rules" for picking excursions and whether to go with the cruise line's offerings or book it yourself (which can sometimes save you money).
If it's a must do, must see, got to have it excursion--book with the cruise line in advance to ensure you have a ticket.If the port involves tendering, book your excursion with the cruise line. Bad weather, high swells, or other unforseeable problems can deep six your excursion and you may be offered a refund if the tour is a no go because the ship says so..If you like to see the island or port of call and dont' mind the bus ride, by all means do it at least once. In the caribbean you can often get the same "tour" by engaging a cab. You'll see the same sights without the tour guide patter, which, in some ports (Key West comes to mind) is a relief. In many ports you can walk off the ship and book the same excursion that shipmates are on and pay less. And of course you can book directly with the tour operator in advance on line. Find your operators and then check them out on these boards.