Hmmmm...
While I'm drawing a blank at the moment when it comes to the wireframe part, there were several games around that era that allowed for free movement in real time during a combat sequence, with menu-based attacks that were limited by range and positioning. And, personally, I've always loved this sort of battle system
Two N64 games come to mind - Hybrid Heaven and Quest 64. In terms of tone, the former is probably more of what you're looking for. Though it mostly features hand-to-hand combat, with firearms playing a limited role.
On the Saturn, there's always Panzer Dragoon Saga! It also allows for free movement, with the ability to target specific enemies and locations on larger foes. Plus, it's 32-bit, like the examples you mentioned. And also a fantastic game in its own right!
And though I don't know any specifics about this, I think it is worth mentioning that both Parasite Eve and Vagrant Story were made by the same company. The similarities in their battle system may be because they shared some of the same development staff. And the uniqueness of those wire-frame systems may also be something that SquareSoft had patented - which may be why you didn't see other games using it
The Star Ocean and Tales of..
. games are pretty well known for their free-movement combat, too! Maybe even the Dark Cloud series? Definitely not the same as PE, but a similar vibe if you are looking something more fantasy-based like Vagrant Story.
Hope that helps!