I think at the moment we shouldn't be allowed company gear from other companies because we're pretty much enlisting in the army, which was far from what we were doing in FF11. I also think we should have unique gear between them just because it helps differentiate more between players.

Maybe the "better gear from company X" could be alleviated by balance stats differently. Like if Grid gets a INT+20 Body piece, give Limsa INT+20 Legs and Ul'dah INT+20 shoes. It would also be good to avoid overlapping stats with Materia so that more people will find use in Company gear. Of course, this is assuming Unique/Untradeable gear remains unmeldable.

The other option is to have different sets for DoW, DoM, DoL, and DoH, and give them different balances of stats, so someone wearing their company set would have the exact same stats as someone else wearing their own company's set. The individual pieces would be different but the grand total would be the same.