As far as the "best time of year" goes, it's a question of what you want. Winter is when the lemon sharks start piling up, spring is a general shark and turtle pileup, and fall is when the goliath groupers get busy. Summer is just nice dive conditions (provided no hurricanes or nasty inlet runoff).
As far as operators, there are a lot to choose from. Narcosis, Ocean Quest, Walker's, Little Deeper, Florida Scuba Charters, Jim Abernethy Scuba Adventures, Deep Obsession ... that's just the West Palm Beach area and I may have forgotten a couple. Farther up north in Jupiter you have Jupiter Dive Center and Capt. SL8R. I really only have recent personal experience with Narcosis, Ocean Quest, and Capt. SL8R and would recommend any of those, but the other ops tend to get good reviews as well.
As far as the type of diving, it's almost always drift dives - no anchors or descent lines and live-boat drops and pickups. On the slow days you'll have to work, but some times the current can howl at up to four knots. In the latter case, stopping to smell the roses at a wreck or reef section can be difficult. I've seen people who are not used to keeping station in 1-2 knot currents blowtorch through an 80 cf tank in 15 minutes. Water depths can range from ~45 ft at the inshore spots like Breakers to 80-90 ft at the deeper wrecks. Occasionally JDC and possibly some of the other boats will go north to hit the Hole in the Wall on the Jupiter deep ledge; I think they typically don't go to the bottom but that area starts off at 120 and slopes down to 140.
Marine life - you're pretty much guaranteed to get the usual assortment of western Atlantic tropical reef fishes. Coral growth isn't as spectacular as the better-preserved Keys reefs. What the area does have in spades are big critters. During the sea turtle nesting and mating seasons (generally springtime) the reefs are coated in them. Loggerheads are probably the most common, with greens and hawksbills also abundant. You might even have a shot at seeing a Kemp's Ridley (which I have) or a leatherback (still waiting). It's possible to run into spotted or bottlenose dolphins underwater. You're almost guaranteed to spot goliath groupers even outside the aggregation season; during it you might just drop in on the Zion Train or Mizpah and have 100-200 all piled up. Some inshore sites like Shark Canyon, Juno Ledge, and Tunnels have a fair year-round pack of Caribbean reef sharks. There are also a couple of sites where resident lemon sharks hang around (note: other boats do feeding trips to some of these spots, so take that into consideration) and in the winter the "out of towners" join the party for an aggregation we still don't have a handle on (it's not for mating and it's not for pupping). In the summer you have a chance at spotting sandbar and silky sharks (typically on deeper sites). If you're at the Hole in the Wall or someone in the group is spearfishing you may have a chance at seeing bull sharks, especially in winter and spring. Tigers and great hammerheads are around, but except at certain sites where they get fed those sightings are rare and fleeting. Even rarer are the Holy S*** Quotient times where someone runs across a manta, whale shark, or great white, but it happens from time to time.
Water temps vary, but generally speaking even an apocalyptic thermocline is going to seem like bath water to a NorCal diver. Winter through spring, I would expect water temps at 68-73. It warms up into the 80s in summer, but you can also have some wicked thermoclines where down deeper the temperature is in the mid-60s. Generally speaking in winter I'm fine with a 4:3 primary suit and the (probably compressed by now) 6.5 shorts-hood-vest overpiece from my old semidry, and in summer I just do the 4:3 possibly with or without a hood. If its a balmy summer day and I'm not concerned about scrapes or looking like white meat to the sharks, I may just do a rashguard and board shorts.
As far as flexibility, one of the reasons I go up that way from Miami is that. The DM will generally be towing a flag buoy, so there's none of that "each buddy team gets a flag" stuff that gets on my nerves in Broward. There's not a lot of babysitting; just hit the water, don't do anything stupid, and come up when your gas/NDL/time is up. You are required to carry an SMB; if you don't have one most boats will have a couple spares (that said, it's a pretty inexpensive piece of gear that has saved my bacon on occasion). If you have a deployable SMB on a reel, even better. I've had a time or two when I've gotten separated from the herd, popped my SMB, and had the boat there waiting for me while I did my safety stop.
