DKaylor,
I ran a rental fleet of Honda Aquatrax F-12's before switching to SeaDoo a few years ago. You should be very happy with them as long as you keep the dry parts dry!
Here is a short list of the most common issues I had with them:
1. I've found that Hondas are relatively easy to roll if not careful. If you start to go over, be sure to pull the lanyard quick or 80%-90% of the time you'll ingest water and hydrolock the engine. You'll need to pull the plugs to evacuate the water (never look down at the motor when cranking it over, you'll get a face full!).
2. Related to tip #1- the rubber boot on the end of the ignition coil needs to be kept lubricated (teflon grease works for me) or it will eventually "seize" on the spark plug and will not come out of the hole with the coil. You cannot get the plugs out if the boot is still on the plug.
3. Also related to roll overs- Hondas have an almost insane amount of sensors. They do a pretty good job of sealing the sensors to keep water out, but I've seen some that get infiltrated. Any water in the sensor connectors needs to be displaced or the machine will not run. What I've done in the past is to spray them down with WD-40 or CRC and let them air-dry. If there is any water in the air box, the sensors will "pick it up" and the machine will only run in limp mode. Pull the cover and wipe all the moisture out.
4. There is a water hose (kind of "S" shaped) that crosses from one side of the ski to the other underneath the drive shaft. While I've never seen it actually rubbing on the drive shaft, I've had to replace quite a few of them when they eventually wear through and start pumping the hull full of water. Note: the ski doesn't need to be running to backfill the hull- just sitting in the water is enough.
5. It can be difficult, if not impossible, to get OEM Honda watercraft parts unless you have an authorized Honda watercraft dealer in your area. The closest to me was 2 1/2 hours away- another reason I went to SeaDoo (2 dealers close to me).
6. You can expect to spill a good amount of oil when changing the inverted filter. There is not enough room to place a pan underneath to catch it, you'll need to cram a rag under the filter mount to keep oil out of your hull.
Overall I was happy with the Hondas, and I think you will be too. Hope this helps!