Best transport methods in Germany, Austria, Slovenia

OOOOHHHH! Train!!!
Because of the conversations you'll learn from, and the fun you'll have. You don't get that via car or bus.

And planes only allow about 50 lbs of baggage, then its bend over. Cars isolate us from what a place is like. Plus the needless vulnerability of cars, parked or targets of drunk or goofy drivers.

And stay for three nights in each digs. Hopfully youth hostels, for the above reason for trains.
www.couchsurfing.com is an option, but more folks in der hostelen, babus.

We rest better in familiar surroundings. And, like tourists say about Spain, "The more
I learn, the more I want to know.

Good research for country, regeon ancient history: mucho documentaries through
www.alluc.org and www.popperslist.com

bbc stuff and others. popperslist gives you a choice of google videon, youtube.com, or guba.com

some stream better than others.
You'll know better questions to ask on train rides.
ç(;oD

Within Slovenia and Croatia, buses are often better than trains (although trains are very useful for getting to these countries in the first place). Buses cover a lot more destinations and usually run more frequently, and are well organised. For these countries it generally works out best to decide on a case-by-case basis for each trip which method of transport is better. Of course ferries might also be an option if you are travelling along the Croatian coast.

I took trains everywhere I went, with the exception of taking a bus from Prague to Cesky Krumlov and back. I loved taking the train!

Would a rental car be permitted across country borders like that?

Germany - Austria is no problem. With Slovenia and Croatia you have to check with the rental company. Car rental makes only sense if you can return in the same country. International drop off fees are mostly really high.

If not, are buses prevelant?

In Germany and Austria far distance buses are barely existing at all. Only city and regional buses serving places not served by trains.
In Slovenia and Croatia buses are an option.

Or is it trains going everywhere at every time, like in UK?

The Austrians and Germans will be deeply hurt if you insist that their railway systems are "like in UK".