Ljubljiana to Zagreb

I'd certainly take the train - took it the one time I traveled directly between cities. There are 3-4 direct trains a day as I recall. There are direct buses, too, but I prefer trains in general. Some of the train ride is really pretty. There is a passport check at the border but for Americans it should be routine - the agents may get on and do the passport check while the train continues moving. A bus would have to stop in the same boarder traffic cars have to deal with. In recent years, there have been occasional long border delays for motor vehicles though I'm not so sure that's an issue anymore.

Yes, the train has a few stops but not many.

This may help:

http://www.slo-zeleznice.si/en/passenger-transport/travelling-abroad/croatia/zagreb

Get on Google Maps and find walking and/or public transit directions from the train station to the Hotel Palace. There are trams that take you from the train station to the center of town, but Google should find you the best way to get there. Google Maps on a smart phone has saved me tons and tons of time navigating towns like Zagreb, on foot or by tram/bus, in real time. I get off the train, ask Google Maps for directions to my hotel, and it tells me which bus or tram to take now, how to walk there, etc.

Direct trains and a few direct buses each are scheduled to take 2 hours 15 minutes and reflected on the Deutsche Bahn link at Looking Up Train Schedules and Routes Online. There may also be competing bus services. The early train is the tail end of an overnight route (with sleepers and 2nd class seats), so it could possibly be in a bit of disarray, in which case you might prefer an afternoon departure. You can buy tickets there locally for about $10 in 2nd class or $15 in 1st; no real need to book ahead.

We just took this train but from Zagreb to Ljubljana in October, and it was fine. Not a fast train, scenery is great, older cars but comfortable. Yes, you lose about 20 minutes for 2 n]border stops (one leaving, and then one entering), but it's really no big deal. We walked up and bought our tickets at the Zagreb station the afternoon we arrived. Both stations easily walked to off the town centers.

Thanks all - very reassuring! A friend also suggested a driving service called GoOpti.com Has anyone heard of or used this service?

It's a well-known service in Slovenia, probably the largest shuttle operator in the country. Their service demands some timing flexibility from your part unless you pay extra. Your hotel in Zagreb seems to be close to the train station, so there may not be as much added value in a door-to-door transfer unless you need the transfer at a certain fixed time and are willing to pay for it. It also isn't that much faster on this particular route as you will likely be picking up and dropping off other passengers around Ljubljana and Zagreb, adding to the transfer time.

Thank you, Dejan. It sounds like the train is the way to go!