This horse is so dead that it should be raised from the dead and then beaten again... but imma say it anyways. IC needs a boost in significant and there's a very simple way to do it.
The solution isn't to separate it from Cyrodiil PVP but rather to integrate it more tightly. Do the following and I can guarantee you IC will become more relevant and fun again:
Controlling all 6 IC districts should give your faction 5% Additional AP in all overland PVP content (Cyrodiil & Battlegrounds). Simple as that.
Yeah the movement and transition between zones needs to be worked on because it's a whole jumbly mess but the hotfix for IC is literally the above.