I think crashes also differ per faction a lot. I remember I had the same problem in my Makedonia campaign, whereas in my current Qart Hadastim campaign, I still do have crashes, but not nearly as many. In fact, I would even go as far as to say it crashes an equal amount of times as vanilla RTW, which does also crash a lot, mind you. I've only had 1 crash as a result of a rebelling settlement (solved by the population cheat) and only a few crashes after battles (even though I never wait with clicking the 'ok' button after winning). Most crashes were during loading.

Come to think of it though, I did play my Makedonia campaign on a different PC, so that is also likely to be a factor.