Actually Tihany on Lake Balaton is pretty even in October and is achievable by public transport but complicated and a little long; and there are a number of other towns that are interesting along the lake. But i think including a couple of train changes it will take you 10 hours to reach any place on the lake while direct to Budapest is about 8 hours.
Another very interesting town with great history is Szekesfehervar. It's about 7 hours direct from Ljubljana and another hour or so into Budapest. http://en.wikipedia.org/wiki/Sz%C3%A9kesfeh%C3%A9rv%C3%A1r#mediaviewer/File:R%C3%A1c_utca,_Sz%C3%A9kesfeh%C3%A9rv%C3%A1r_02.jpg
You can also get a direct train to Veszprem in something less than 7 hours. Veszprem is a nice town we have visited a couple of times, and it is where you can rent-a-Russian-tank, if that sort of thing lights your fire (my wife had a blast).
I love Pecs, but again, getting there by train from Ljubljana is less than wonderful. Of course on all of these I haven't check bus routes, but I am not a big fan of the bus.
You also might consider putting the time in Budapest then running some overnights and day trips our to Budapest. There are great places to visit out of Budapest in about 3 hours or less each way. Pecs is high on my list, Eger would be great in October, I love Gyor (Archabbey at Pannonhalma), Sopron, Kosice (Slovakia), Szekesfehervar. The difficult thing about Hungary is that Budapest is the rail hub. By train you cant just tour the country, you have to return to Budapest between most of the good places to visit.
Mid September to mid October is my favorite time in Budapest. We'll probably be there about the same time as you.