2 days in Croatia-Advice

Plitvice is a great start. It's about 2 hours from Zagreb. Island sightseeing from Zagreb, not so much. Zagreb is very much retreated from the coast. If you're going to Venice by boat I believe you'll need to be staying near Pula in the Istrian Peninsula. There may be other departure points, but not sure about that. But if you need to leave from Pula then you really won't be seeing any islands. There are some small islets nearby, but that's about it. But seeing that you have to make your way from Zagreb to Pula by driving (I'm assuming) that would take at least 3 hours. So you're best bet is to start really early in the morning.

I don't think you have enough time to see much in the way of islands, unless you head straight to the coast after your Monday in Plitvice. There are islands like Krk and Rab off/near the Kvarner Gulf (near Rijeka), but most people talking about islands are thinking of those off of Dalmatia to the south. You could overnight in Optaija or Lovran and try to do an excursion to one of those islands then head to Rovinj or Pula by Tuesday night, if you think it's worthwhile.

I'd probably just go from Plitvice to Rovinj and ferry from there, depending on the time of the year. There are ferries directly from Rovinj to Venice daily in high season but only a few days a week in September then none after the first few days of October (you didn't say when you are going). I greatly preferred Rovinj to Pula. If you can't get a ferry, you can also take a bus from Pula or Rovinj to Trieste and a train from there to Venice.

After landing in Zagreb, will you have a car to explore Croatia or will you be taking the bus?