2weeks in Slovenia/Croatia - comments/suggestions pls?

It's a face-paced itinerary, but it should work.

Regarding your time in Slovenia: do you mean you have two full days in Ljubljana and a day trip one day, so four nights or really three nights? If you have four nights then yes you can probably cut a night there. But if only three nights, including an arrival day from Asia, I would not cut a night there.

I wasn't crazy about either Zagreb or Split, so no, I'm not personally wondering why you don't have more time there. Some would urge you to spend more time in either or both places, because they like those places more than I do. But I'm not sure how much of Krka you plan to see - it is not compact like Plitvice is, it is more spread out. You could see just the Skradinski Buk waterfall instead of taking the whole day to see everything else (there's a boat excursion I think, I saw only Skradinski Buk) and that would give you half a day in Split anyway; if you will have a full day in Krka, you'll probably arrive too late in Split to see anything, which would be a shame.

Your day getting from Zagreb to Plitvice to Skradin by bus will be a long one, and to make that work, you'll have to get up at the crack of dawn to catch the very first bus out of Zagreb, because the last one to Skradin out of Plitvice is at 15:15 according to the site I checked. That's doable - find a place to leave your bags at the park, get into the park before 9:00, get back to the bus stop by 15:00 - so about six hours to explore Plitvice, but you will have no time for error. I'd probably recommend staying over in Plitvice instead of Zagreb, so you can get up a little later, assuming you can find a vacancy at one of the park hotels for September by now (maybe not). It would be nice to spend a night in Zagreb, but if you have to get up so early, you probably won't be up very late the night before anyway.

I like Zagreb a lot, but expecting to get up in time to make a 6 AM bus...for me, that would be a dreadful idea. The bus station will probably be a significant walk from your lodgings. It's much safer to spend the night before your Plitvice visit near the park so you're certain of being way ahead of all the daytrippers on the walkways. It makes a huge difference in your experience. You're going to the park on a Friday, which I think may be busier than Mon-Thu, though I'm only guessing about that.

One option would be to arrange to store your bags at your Ljubljana hotel while visiting the caves and then relocate to your Bled hotel that night. However, I found Ljublhana very charming and much livelier than Bled, so I'd prefer to have the evening in Ljubljana.

Check with the tourist office upon arrival. I think there are weekend markets in Ljubljana (both near the rlver) you might be interested in.

Before finalizing anything, verify that there will be buses running to (or at least near) Skocjan on Sundays in September. That could be a problem.

I agree about Ljubljana - I loved it. It's a great place to come back to at night. The town of Bled is nothing special and not particularly charming, so it's not much fun in the evenings, but it does make a more convenient base for exploring Lake Bled and Lake Bohinj and surroundings.

Thanks Andrew H. and acraven for your input! Really appreciate it

• For Ljubljana, it would be 3 nights :) I'll be visiting the Skocjan caves on a tour so they will drop us back at the hotel in the evening so no worries on the luggage storage and transport :) I believe there are some markets as well, I will check them out.
• For Zagreb to Plitvice, yes I attempted at first to stay a night at Plitvice but there are no more accommodation options for within the park :( and because we are not driving, it does not make sense to be staying at the nearby towns as we will still need to look for transport to the park so Zagreb was the only option. We are aware it is going to be a little awful to catch the first bus at 0545h but we will be putting up at a hotel just minutes walk to the bus terminal and hopefully we get to catch some sleep on the bus there - hopefully all these to get some time before the crowd comes in is worth it!
• For Krka, to be honest, I've not had the chance to map out the route yet but yes, I'll consider the half-day option at Skradinski Buk waterfall. There seems to be only bus options departing at 1400h or 1700h left though.
• After much reading, I'm inclined to Vis over Korcula. I will leave Vis for Dubronik on a Tuesday and I read somewhere there's a ferry we could catch to Dubrovnik via Hvar. Where can I find out the schedule and book tickets for this route? Also, the catamaran/ferry rides that cover the Dalmatia, they are not bumpy rides, are they? As I tend to get seasick quite easily.

One option between Zagreb, Plitvice, and Split: there's at least one tour service that offers a transfer between Zagreb and Split with a stop at Plitvice for a tour. I've not used such a service, but you can google them.

Then could spend two nights in Split instead of one and take a day trip to Krka. I know that's a bit of extra backtracking, but it might make things easier: not have to worry about the bus schedules and getting up so early to catch one in Zagreb. But then again, I have no idea what time they pick you up etc. And you might get a little more time in Split perhaps. Worth checking in to, though.

I've not been to Vis, only to Korcula. I took a catamaran from Korcula to Split (via Hvar). The ride was OK but probably it's a bit weather-dependent.

I personally don't think you have enough time in Dubrovnik with the day trips or for the islands. I would look at travel times to determine how much of your last few days you will spend in a car/bus/boat. Also keep in mind that September (like end of May, when I was there) is the shoulder season and ferry trips are much less frequent then. I would look on Jadrolinja's website to determine what is possible. It will also depend on whether you want a car ferry or a people-only ferry.

I would also come in through Istria (skipping Zagreb) on your way to Plitvice and further down the coast.

They are all lovely places and I think you will LOVE them all!

Go with Korcula. Two nights is really not enough for Vis because the ferry takes longer, the transport is not great, and it will be very quiet in September.
Catamarans are operated by Krilo and ferries and catamarans are operated by Jadrolinija (google for websites) and note you can also take a bus from Korcula to Dubrovnik (bus takes short ferry).

Driving is very easy and great way to see nature. If you did you could drive from Lake Bleb over the Julian Alps and be near Predjama Castle and Skocjan caves then go to Rovinj. From Rovini go to P. Lakes. Thought Split was a great place to visit. But above depends on you driving.
You can see my pics of a similar trip a my personal blog.
http://www.gadtravel.com/2008/10/slovenia-and-croatia.html