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As far as i'm concerned there is no legitimate reason. I've taken on clients that have previously had this scenario and it's absurd. The client, i.e. the ADVERTISER owns the data in that account so agencies should access a clients adwords account via an MCC, that's what an MCC is for!

In EVERY case where i've seen agencies use their own accounts, the client has received flaky reporting and had no real understanding of ROI. If an agency knows what it is doing, it should have no problem doing it properly.

I usually explain to the client from the beginning:

If you want long term, sustainable results then we're your guys. Like everything that lasts long term it takes time to build foundations that last so expect to see results slowly build rather than appear overnight.

If you want overnight results and risk the rug being pulled from under your feet, then we're not your guys. We only want long term partnerships.

Tends to work well when most other SEOs are preaching the "We'll rank you number 1 in 30 days" crap.