Custom Reports are my biggest gripe with the beta.
1. The report preview function was removed in the beta. This causes me a great deal of pain as I like to create custom on a completely ad hoc basis and only save the reports that I feel I will use at a later date. In the beta, everything is saved and I get a bunch of clutter reports I will never use again.
2. Secondary Dimension Drilldowns are still missing from custom reports. This is a big issue for me.
3. It looks like pivot reporting has been added back to the regular canned reports, but has not been added to custom reports.