Hi fomalhaut,

Yes, it should be save game compatible, the only thing you might notice is the change of some unit sizes depending on what faction you're currently playing, though I will admit up front I haven't tested this...

As for your fundamental issue, I would recommend playing with Alexander, as what you describe sounds like an AI problem and this only modifies unit stats and a few other things. I haven't had any major problems with the AI engaging, as far as I remember.