First, do not use an epoxy "paint". There will be issues with bond between the steel and the coating. Epoxy-coated rebar is fusion bonded (think powder coated), which is applied within seconds of being sand blasted, and a quality assurance process still is required to be sure the bond is sufficient.
Second, connecting coated and uncoated bars results in a macrocell corrosion potential. This is where small holes in the coating result in significant local corrosion because the relatively large uncoated bar acts as an anode, sinking free electrons which would be "trapped" within the coating of an isolated, fully-coated bar. Corrosion is an electrical process, and the coating acts as a barrier to flow of electrons.
Do not partially galvanize anything. This will result in the partial zinc coating acting to protect both the coated and uncoated bar, leading to premature oxidation of the zinc, resulting is loss of protection.
Epoxy-coated bar is not really very expensive, particularly since you are not talking about a large quantity.
As to the epoxy bashing, there are 100,000 bridge decks in the US using epoxy-coated bar. Of these, fewer than 200 have experienced premature deterioration. The product is used every day in every state, because it represents the best value for tax dollars under most circumstances. Where the exposure is severe or construction is expected take its toll on the coating, stainless is frequently used. Galvanized bar is also very good in most applications requiring corrosion resistance, but provides limited protection in some conditions (the zinc coating is sacrificial so the life is limited by that.) The first line of defense against corrosion is proper cover and concrete quality. Make sure there is proper consolidation and shrinkage is minimized to avoid excess cracking.
The problems in Florida and Hawaii were related to handling problems, and macrocell corrosion where black steel was mixed with epoxy. Both of these are addressed in the relevant design and construction standards, some of which were changed when macrocell corrosion was identified after these events. Handling is addressed in industry publications and the ASTM A775 spec. The coating is tough, but if they tear up the coating during construction, it certainly can't be expected to work properly. FHWA has long term projects which are showing good performance of galvanized, epoxy, and stainless bars under very harsh conditions. We expect publication of these findings very soon.
