Hi Yoav,
AdWords Scripts is limited in its feature support, and is most useful if you want to automate your campaign management to some small extent (e.g. run some reports, adjust some bids, upload some keywords, etc.). On the other hand, if your requirement is more full-blown (run your own SEM platform, make changes that run into hours, fine control over what accounts to process and when), you should look at AdWords API. AdWords Script runs and scales on Google Servers, whereas AdWords API has to run and scale in your own servers.
Cheers,
Anash P. Oommen,
AdWords Scripts Team.