One problem is inappropriate ads. You don't want spammy junk advertised on your site. Google's standards probably aren't as high as yours. You can filter out 200 URLs, but in some industries that won't be enough.
The stats Google supplies are inadequate. They're easy to understand at a glance. However, they don't tell you exactly which ads people are clicking on, or which keywords are involved. That's frustrating.
Also, I'd like to be able to identify and block ads that have very low payout rates, without doing a lot of sleuthing and messing around.
The ad panels say "Ads by Google" - free advertising for Google. You don't earn anything if someone clicks on that link.
The minimum payout is $100, which is regarded as too high by sites which don't receive much traffic. That won't worry experienced webmasters.
Also, sites that want to display AdSense ads may not include "other content-targeted and/or text-based ads on the pages displaying AdWords ads." However, human beings review the sites. Rejected sites have been able to appeal successfully.
Another disadvantage is that Google doesn't allow you to share your stats with other webmasters. The AdSense Terms and Conditions say:
"Confidentiality. You agree not to disclose Google Confidential Information without Google's prior written consent. 'Google Confidential Information' includes without limitation: ... (b) click-through rates or other statistics relating to Site performance in the Program provided to you by Google..."
That's really weird. Web site owners need to be able to share such information and discuss successes and failures.
A big disadvantage of the service is that Google doesn't say how much its AdSense partners will receive. You'll just receive an unknown share of the revenue.
Only a company with the goodwill and respect Google has earned could get away with such a cheeky offer.
Google says:
"How much will I earn through this program? The AdWords ads you are able to display on your content pages are cost-per-click (CPC) ads. This means that advertisers pay only when users click on ads. You'll receive a portion of the amount paid for clicks on AdWords ads on your website. Although we don't disclose the exact revenue share, our goal is to enable publishers to make as much or more than they could with other advertising networks."
So the only way to know how much you'll earn is to try it and see. If you want to bail out, all you have to do is remove the code from your site.
Don't put all your eggs in the AdSense basket. If Google discovers fraudulent clicks on ads appearing on your pages, it can dump your site from the service, and refuse to pay you all revenue owed. Some webmasters who claim total innocence have had this happen to them.
Google has made several changes to its AdSense FAQ, clarifying varying things. For example, it IS possible to apply for separate accounts for separate web sites. I've done so, and checked with Google that it's OK in my case. Read the rules - they look ambiguous to me. If in doubt, ask first!
Some time after the launch of AdSense, Google added "channels" which improve the tracking. I strongly recommend that you experiment with these.
Sites with "excessive advertising" are being rejected.
PLEASE read the rules and FAQ. When I looked, some advice in the rules contradicted advice in the FAQ. If in any doubt, ask their support staff. They're very helpful.