Like the rest of ST, take whatever you want from it. Personally, I assumed that "The Enterprise Incicent" was a follow up to "Balance of Terror." The language describing the cloaking device as "new" was simply theatrical. The evelution of the cloaking device was a indicated in a TNG episode where the Enterprise is sent to intercept an old Klingon BC whose crew had been in stasis for 70 years. There, it just made sense that an older device would be obsolete.
As far as a perfect invisiblity device, as portrayed in ST4, that's almost more of a comedic device than sci-fi. The weapon ranges and speeds of starships would make visual combat a rediculous notion. As we experience ST as visual media, the visual effect of invisiblity and the combat effect of disappearing from targetting sensors are one in the same, but any military wargamer knows that these are entirely different concepts. To critique the movie on this line is pointless, but to form rules for games and such, the films have to be taken with a grain of salt.
Personally, my take on the cloaking devices in TOS is that they were essentially the same thing. If the device in "The Enterprise Incident" were an improved model, that's well and good, as well. I would expect; however, the cloaking devices encountered by Picard and Kirk to have as much in common as an F-22 and a P-51. There would have been intermediate devices between the first one encounter and the last.
Anybody trying to make sense of what is produced for theatre is running a fool's errand. Film and television writers and directors are free to do whatever they want to produce a whatever theatrical device they feel like. They create errors and inconsistancies while they correct errors and inconsistancies from TOS. It's all make believe, so put the technology together inside your head however makes the best sense.