We've been diving in Costa Rica twice so far, and are going again in September. We haven't made it north to Guanacaste yet - we'll do that on our upcoming trip.
We're kind of doing things backwards, though - I believe most people probably dive Guanacaste first, as it's the region that is much more well-known, and has many more dive sites and operators. While we haven't been there yet, my extensive research indicates that the diving is going to be best up north, when you factor everything in - convenience, cost, etc. There are several dive shops and quite a few nice hotels and resorts in the area, and you can get some great packages (I'm doing my own research on that now - I'm looking at some packages that include 7 night stays and 5 days of two-tank dives for $500-600 pp - great deals!). I'm especially looking forward to getting out to Catalina and Bat Islands.
However, Isla del Cano in the south has much to offer as well - especially if you are looking for a dive spot that is truly undiscovered and off the beaten path! The visibility was great, LOTS of marine life, and a very healthy underwater environment...and NO crowds of boats fighting for the same dive spot. The only problem with Isla del Cano is its remoteness -- to dive there you have to either stay at one of the few hotels in remote Drakes Bay, which are difficult to reach (especially in the rainy season), or take a rather hairy 2.5-hour boat trip there on a small, open craft, pounding through pretty heavy seas. I believe there is still only one dive operator doing that trip - Oceans Unlimited out of Quepos. The diving is truly spectacular, but it is rather costly - $200 per person for a two-tank dive!
We've also been diving locally off Manuel Antonio Nature Preserve, which I would put at the bottom of the scale. The visibility wasn't great and there was much less to see.
Hope this helps!