Some ferries and catamarans run year round. I would lay out a specific agenda first, then figure out if you can do it without a seasonal ferry or catamaran. You won't know 2018's ferry schedule until 2018, but you can guess based on this year's.
With only two weeks, you aren't going to have a lot of time to do a bunch of island hopping if you are including Ljubljana. So not many ferries may be involved. A basic itinerary of say Dubrovnik, an island like Hvar or Korcula, Split, Plitvice Lakes, Zagreb (or Istria) and Ljubljana can certainly be done in May mostly by bus (or rent a car for the Croatia portion and take a bus or train on to Slovenia). You may have more options for catamarans in the summer that make it easier to get from place to place, most likely.
You are always playing the odds with the weather. I had decent weather mid-May two years ago when I visited Croatia, but you never know. As you get into June it will get more and more crowded. I'd guess better weather in June than May, based on the odds, but also more crowds on the coast.
