It looks like I am going to have to replace my 16 year old AC shortly. I have a vertical air handler unit in my garage. It takes up a lot of space and is built on a wood box and it continually has moisture issues. I have been looking at changing from a vertical unit in the garage to a horizontal unit. Does anyone have any insight if a vertical unit would have more issues than horizontal units? Or any pros or cons? Thanks for any insight.

As far as condensation drainage, vertical better.  Especially if you are talking about putting in an attic instead of leaving vertical in garage.

Your going from on unconditioned space to another will gain you nothing.  Get at least three quotes and see if anyone addresses your duct work as part of the problem, airflow is key in AC working properly and most likely you have a restrictive duct system.  Newer AH will have more insulation and be sealed better if installed properly.  So if airflow is not and issue and equipment is installed properly you should be good.

A vertical air handler and a horizontal air handler is the exact same piece of equipment.  They are made to be up-flow/horizontal.  If you want to move it up to gain floor space, that shouldn't be a problem unless there isn't room.

Make sure the air handler cabinet is insulated on any price quote you get.  

Personally, I would never use wood in any duct system.  That wood box should be made of sheet metal and it should be insulated inside or out.

Not sure if your "moisture issues" are condensate removal related or duct/cabinet sweating.  Either way a quality contractor should address those at the time of installation.  Mention it.

A quality contractor will run a manual J heat load calculation to determine your needed capacity and not just replace your current size.  If changes are being made in capacity, duct changes will also have to be made.

In Florida insulated duct board is commonly used.
If you don’t want condensation issues make sure that the air handler is in a conditioned space.
Most air handlers are convertible from vertical to horizontal.