What constitutes an important city? Well, most major areas have more than one walled city and all but one faction start with a walled city so no one is seriously nerfed. Important cities tend to be bottlenecks, major trade hubs and historically important cities, like Pergamon, Sinope, Rome, Alesia, Osca etc. But greece is not a siege fest, neither is Italy, the devs weren't Romecentric or Greekcentric, so the amount of walled cities are well spread out over the map.
It does change the focus a bit when you can conquer and lose several in a turn, but that only happens in truly major offensives, since it's better to set a decent garrison to a newly conquered province and began building auxilia than devastate the same province by expanding too quickly and leaving it relatively open for several counterattacks. Another thing you tend to do is trying to conquer important cities the first. Which is actually historical.
It's great, I tried Pontus(which is next to Seleucids and my fav faction in any game) and wasn't instantly run over by Gray Hordes even though I thought I'd be. The thing is that the same problems you have, the enemies tend to have too, so big powers are continuosly harassed(Seleucia and Ptolemaics, Greece and Rome and Macedon, etc) and leave a relatively open playground for the smaller factions.
Except Armenia. It's freaking wacko.
Try it out, you can run Metronaval on the side of Platinum, it's a separate "install".