I hear that Toho had the wires digitally removed before the the theatrical release of MEGAGUIRUS. The R2 release is reflective of that.
The reason they're so visible on the R1 could be a number of factors. While people point to the brightness being the issue, I think it's entirely possible that Toho's international print of the film simply didn't receive the same wire-removal treatment, which is why they're visible. The JP version wasn't simply darkened to hide them. The wires were literally removed, as far as I remember. If the export print wasn't based on this version, then the wires were sure to show up on it no matter what medium you're watching the film on, whether it be via 35mm, or on a DVD.
The only way to be sure would be to either A) See a screening of the international version, and if the wires are still visible, then my theory is correct or B) If another country releases the international version of DVD. So far, the copies available in other countries have all been soured from the "doctored" Japanese print.
Anyways, that was waaaay off topic.
It makes sense cause there would have been two Mechagodzillas in Unleashed, having the II separates it. II makes sense for the normal consumer, as Legionmaster said.
I never believed it was a fan theory, I just didn't know that the international title didn't have the II.
M'kay. This doesn't explain why you're so perplexed about him only being dubbed as "Mechagodzilla" in the film. This isn't a sequel to the 70's film, so why would that moniker make any sense?
Logic. Use it.