Croatia, Slovenia, Bosnia in Winter?

I cant imagine doing that much in 14 days. I will say that while the bay front between Dubrovnik and Kotor is amazing; Kotor is just a small and less spectacular Dubrovnik. So I would skip it.

Given you are doing this at Christmas I would arrange to be in a major large city with a reputation for Christmas activities two days prior to Christmas eve so you can enjoy the markets, etc (Vienna, Budapest) then stay in that city Christmas Eve, Christmas Day and Boxer Day as those days most things will be closed. The larger the city, the greater the odds of finding things to do on those days.

As Croatia is so wonderful in spring, summer and early fall, i would save it for a trip at that time and concentrate in the winter on locations that shine in the winter.

This feels like a bit too much moving around to me, and I think it will be very difficult if you do not have a car, because you'll spend a large portion of your time either on a bus/train or waiting for a bus/train--plus all the time required to pack/unpack and check out of and into hotels. Even with a car, I wouldn't want that many stops.

Most of the time you will pay a great deal extra to pick a car up in one country and drop it off in another, though of course you need to check with a few rental agencies to see whether that applies in this case. If, as I suspect, you find that a car is only viable between Zagreb and Dubrovnik, spend some time Googling to see what sort of bus and train schedules you turn up for your trip segments through Bosnia-Hercegovina and Serbia. And be aware that cross-border buses tend to be infrequent, so you may need to buy the Dubrovnik-Mostar and Sarajevo-Belgrade tickets ahead of time. I have seen such buses sell out, and I assume the possibility increases during holiday periods. For that matter, even the intra-country legs of your trip may be at risk of selling out.

BusCroatia.com was a pretty reliable source for me on buses within Croatia. In B-H and Serbia, it may be more difficult to get solid schedule information before you are in country.

I don't know what range of weather you can expect in late December, though I think you can be pretty much guaranteed of "not warm", and rain will fall on average every 2 or 3 days. I urge you to check wunderground.com for actual day-by-day weather in recent years to see what range you need to prepare for.

I wouldn't prepay for the trip to Plitvice, just in case you get unlucky with the weather. It is lovely, but it wouldn't be fun in heavy rain. Also note that the usual recommendation for Plitvice is to spend the night before your visit near the park so you can get a very early start due to the expected severe overcrowding. In late December, I assume the number of visitors will be way down, so I hope you'll be OK doing the park as a day-trip from Zagreb. One advantage of doing so is that if the weather causes you to skip Plitvice, you'll find enough to do in Zagreb, which has a variety of museums as well as a nice historic district.

If you have extra time while in Belgrade, Novi Sad can be visited as a side-trip. The historic district is quite interesting, though you'll probably want to take a bus or taxi from the bus station.

Thanks for the advice!
I've cut Belgrade out in the interest of time, and here's my updated itinerary (14 days now!):

19/12 Fly into Ljubljana AM - day in Ljubljana
20/12 Day trip to Lake Bled
21/12 Ljubljana
22/12 Ljubljana train to Zagreb (PM)
23/12/ Zagreb
24/12 Zagreb
25/12 Zagreb -> Plitvice Lakes
26/12 Plitvice Lakes -> Split (AM)
27/12 Split
28/12 Split -> Dubrovnik (AM)
29/12 Dubrovnik - potentially Kotor day trip??
30/12 Dubrovnik -> Sarajevo (stop at Mostar otw, yes or no?)
31/12 Sarajevo
1/1 PM flight back home

*planning to drive in Croatia to save time

So essentially I have about
2.5 days in Ljubljana,
2 days in Zagreb,
1.5 days in Split
1.5 days in Dubrovnik,
1.5 day in Sarajevo

• does this breakdown look ok or should I be reallocating?

So my questions are:
1. Should I skip Mostar and Kotor?
2. Does the breakdown look ok or should I be reallocating the days?

Skip kotor.

I would allocate the least amount of time to Dubrovnik (1 day max). It's way too small to give it as much time as Sarajevo and even Split. Frankly, I would skip it and devote that time to Sarajevo which has much more to do and is a fairly large city. I loved Mostar so if you can stop on the way, then great. I think the public transport in winter may be challenging in terms of frequency (I'm not sure but just a guess based on my trip in September) and you've really got a schedule that's really aggressive and assumes that you have solidly good and frequent transport between your sites. I don't know what Dubrovnik would feel like in the winter - also keep in mind that Sarajevo will be much, much colder than on the Croatian coast.

Just did some research on Split and it looks like most of the activities operate in summer. I'd really like to visit the Blue Caves but again, that's only available in Summer. I'm thinking of cutting out Split altogether - what do you think?

In higher elevations you will encounter not just rain but probably snow and if you are unlucky then lot of it.

Just did some research on Split and it looks like most of the
activities operate in summer. I'd really like to visit the Blue Caves
but again, that's only available in Summer. I'm thinking of cutting
out Split altogether - what do you think?

I think that I wouldn't go to the Adriatic Coast in the winter. I would concentrate on places either MUCH warmer (of which there aren't many in Europe), or much colder with an active winter orientated culture. That means mountains or cities.

Just returned from my annual trip to Croatia. My wife grew up in Bosnia and we have been to Sarajevo and Mostar and other places on your Croatia list many times. First, I would not go to Sarajevo in winter. The valley fills up with woodsmoke from all the stoves, and air quality can be an issue. Also the outdoor market and cafes are far less fun in the cold. Sarajevo is too powerful an experience.to add winter woes to it. Go in spring or fall for better weather and everything open and humming.
Mostar however is an easy day trip from Dubrovnik with a bus tour. Do not drive into Bosnia, even if the road to the coast is easy. Cars get stolen. I would go to Mostar only. A taste of Bosnia and a lot to see. Consider hiring one of the local guides, it makes all the difference - see names in Rick's Guide to Croatia, which has a picture of Mostar, Bosnia, on its cover thanks to the publishers' lack of culture. Local guides can be called by any TZ or Tourist Office. The TZ in Zagreb is on the main square - INFO.
Advent in Zagreb is a BIG DEAL. Google the Tourist Office website. I love Zagreb, and in winter it has museums, art galleries (my fave is the Museum of Naive Art in the upper town) and cafes with rugs and heaters and indoor areas. Zagreb has Bornstein's famous wine cellar up past the Cathedral, now offering wine tasting and education that really explains not only wine, but Croatia in many aspects.
New Year is a huge deal in major cities, and major hotels offer special packages. You may want to secure your bookings just in case.
You can check the bus routes inside Croatia on Autotrans.hr which has an English version (click on the UK flag in the corner). Make sure to buy both ticket and reservation for a numbered seat (numbers above or on the the seat armrest) or you will be bumped out. A luxury bus line is run by Deutsche Bahn (DB) and their express buses serve Germany, Ljubljana and Zagreb. Fast trains run to Split.
Spending more time in a few main cities will help you learn their streets,, making it less scary and more fun.Less is more. If you have no bookings in Zagreb yet, splurging on the Hotel Dubrovnik puts you right in the heart of town in a modernized hotel. Your route may involve taking a flight back to Zagreb from Dubrovnik, in which case you could stay there twice.
Be aware that large festive crowds in any of the cities are opportunities for pickpockets, and dress and stash valuable accordingly.
But make the most of Advent in churches and in Advent markets and celebrations - it is is a time to eat, drink and be merry! Chestnuts are roasting on street corners, good coffee, chestnut puree cakes and a rich selection of food and drink is available. Carry Kuna cash from the nearest ATM machine, and tip your servers. They need every penny. Introduce yourselves by name, and ask theirs. Enjoy!

I just left Sarajevo and I loved it in winter. It is cold, but was nice not having a crowd. I took a day trip to Mostar, but given your timeframe, I would skip it (it was fine to see but I enjoyed Sarajevo more).

If you do go to Sarajevo, I would highly recommend Hotel Konak where I stayed (http://www.konak.ba/v2/local/index.php). The location is right in old town, it only has about 6 rooms, and the staff was amazing.