The main reason is the better usability of the MV. (Mainly the way the use of mouse inputs enhances the playing experience)
This is especially true for the Battle System, where a single click on a skill and one click on the enemy status or position executes that skill, compared with browsing through multiple sub menus in the VXAce version. This is also true for other systems.
The RTS version of the Warfare System I worked on as a mini project to test it out and learn JS for the last half year ended in disappointement.
I did produce a working demo, though the feedback was mixed at best and the usability was just not there. So warfare will be implemented in a much more spreadsheet like fashion or droped from the game entirely.
I do plan to release demos of the new version as soon as the first main systems are done, instead of waiting for the completion of the first chapter.