You can't go wrong either way, as others have said.
If you opt for the North:
I like both Ljubljana and Zagreb a lot and would have a hard time choosing between them. Zagreb is hilly and much, much larger (a negative for some) but seems to have more top-flight museums. Ljubljana has a small river flowing through its center, which is always pleasant, but the area around (not inside) the historic district has a noticeable graffiti problem. I think you'd enjoy either city.
Try to schedule Plitvice Lakes on a non-holiday weekday, avoiding Friday and Monday if you can. It was overrun when I visited on a Friday in late August. You can do the park via public transportation from Zagreb if you want to save some money. Pick a non-rainy day, obviously.
I stayed in Rovinj in Croatian Istria. It is very touristy but very picturesque. Took a day trip to Porec, which looks quite different but is also very touristy. Vrsar is smaller and up on a hill; it can be combined with Porec, but get an early start if you're using public buses. I really enjoyed an Island Istria day-tour that looped through the interior. You can pick it up from Rovinj and other coastal towns. It's difficult to see the interior via public transportation.
In the South:
I visited this area 20+ years ago, so this time I pretty much blasted from Montenegro straight to Zagreb. I broke the bus trip in Zadar and can confirm that it's very nice to visit. It's a manageable city with a very picturesque old quarter. Not undiscovered, but I think it's lightly visited by Americans.
On this most recent trip I stayed in only one hotel. I found the Croatian B&Bs, apartments, etc., to be modern and comfortable. However, if you're non-smokers and sensitive to cigarette smoke, I'd caution you to be careful about rooms located in people's homes. It's not something I thought to ask about, and I ended up spending a couple of nights in a very nice bedroom+bath upstairs in the home of a heavy smoker. Houses just aren't built to contain cigarette smoke like (most) hotels are. If a booking site says a property is non-smoking, there's no guarantee it has never been smoked in, but it's probably safe to assume that the resident owner doesn't smoke. Or so one would hope!