It depends where you're planning to go. I don't think that it's a good idea to force yourself to avoid certain lines, merely to save a few pennies on fares.

Even if I had a Metro pass, I'd probably still buy a SUICA on the first occasion that I wanted to ride a non-Metro train.
You can get a refund on the SUICA at the end of the trip. In the worst case, you may lose ¥210 (JR's charge for refunding unused credit). If you're smart, you'll find a way to run the stored credit down to zero before asking for a refund on the deposit (no charge for that). To me, the added convenience is worth it.