I'm all for removing the exploitative abilities of PDC's as well as making ground combat more interesting. However I think outright removing PDC's would remove some of the interesting possibilities that the new ground combat mechanics might develop.
For a start remove the potential for exploitation, make them require maintenence, which will stop them being exploited, and allow enemy PDCs to be blockaded.
Give them a deployment time. Sure you can just increase crew quarters to raise deployment but that would also increase maintenance costs.
Large ground battles in the area should damage the PDC's armour, or perhaps there should be some kind of titan that excels at damaging PDC's, or provides addittional combat effectiveness to engineers.
One problem I have with PDC's is that a well equipped PDC that's actually vulnerable to being taken out with a small ground force is still basically invincible if it can swat every shuttle out of the air before it lands.
It needs to be somewhat easier to get small forces onto the ground to contest a heavy anti ship weapons facility than currently possible.