November weather will be mostly cloudy and rainy in inland areas of the Balkans, I'm afraid. In terms of weather it's better suited for cultural and historical attractions rather than nature, which is the absolute highlight of the Balkans IMO. That said, there are some enjoyable weekend trips that you could do. Although not on your list, Belgrade has a night train connection with Thessaloniki and has plenty of things on offer to keep you busy for a weekend.
Unfortunately, continuing further north or west to the other countries on your list will take the best part of the following day, so Belgrade really is as far as you can go by train to still make it feasible as a weekend trip. Anything further than that will require flights due to the sheer distances involved. The fact that many Balkan countries have relatively poor transport infrastructure and mountainous terrain does not help with transit times, either. Also, I encourage you to think of cities or specific areas as possible destinations, not whole countries. A weekend trip is a very short trip, you would basically be visiting one city or two nearby places at most.
Perhaps you could rent a car in Thessaloniki and visit some places in Bulgaria for the weekend? I'm not sure whether rental companies in Greece allow their cars to be taken into Bulgaria, but that strikes me as a relatively easy option, if possible. Macedonia is also realistic - visiting Lake Ohrid, for example. Generally, the more to the south you stay, the better the weather is likely to be.
As flights go, you would need to look into flying to the country of interest, with the exception of Slovenia and Istria in Northern Croatia. For those two areas, also look into flying to Venice Marco Polo, Venice Treviso, or Trieste in Italy, as well as Klagenfurt or Graz in Austria (only for Slovenia). You can then continue to Slovenia or Istria relatively easily by bus, train or shuttle transfer (www.goopti.com), or even by renting a car for the weekend. Although Vienna and Munich are popular options for travelling to Slovenia, too, they are a 3.5 and 4 hour drive from Ljubljana, respectively, too far for such a short trip.
