Fluid changes are much more expensive with an auto. A manual just requires a quick drain & fill with 2-3 quarts. An auto takes 3-4 times more fluid if flushed, plus a filter which requires dropping the pan.
I'd still say a manual is cheaper in the long run. I'm planning on getting at least 200,000 miles on my clutch. My aunt got almost 300,000 on her 98 Corolla.
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