Still working on counter-tactics: the motion mines MUST be cleared with the Zeller from above. I tried to clear them with the AE diffuser from below and from above, and it's too far. I tried clearing the with the Zeller from below, and no part of the mine sinks through the shield. Mines can be cleared from the outer shield by the same method, since the part of the titan that houses the AA guns is outside, so you can climb up there and snipe them off.
On a side note: I also tried the motion mines in the core thing, and it does NOT work. I was on a local server (unranked) with FF on, captured all the silos, killed all the undefended consoles, and placed mines at the base of the core. Then I switched teams, and took off in the chopper. Flying circles around the titan and landing on the back deck resulted in no damage to my core. When I ran inside, they were still there where I had left them, so they hadn't been activated by my chopper.