The same topic came up after fying was introduced in WOW, so in the latest expansion they grounded all the mounts. Needless to say it didn't take long for people to want flying back. Long term effects of removing flying in WOW? Well you have probably seen WOW's subscriber numbers dwindle in gaming news..? Bottom line flying is awesome especially to people who can't play a lot, which is most of FFXIV's player base.

Also I'm not saying flying is the only factor in WOW decline.