Here they are:

1. There’s no lack of money for a conveyance (canal or tunnel). The water it would carry is far more valuable than the cost of construction. There’s a lack of political and legal agreement on if it should be built and whether it’s possible get get approval to build it.
2. Any conveyance (esp. one with a 15,000 cfs capacity — 10 times the 1.5 maf capacity of the Colorado River Aqueduct) is going to affect water flows. It may make things better — reducing the need to pump water and the volume of water that has to be send through the Delta — or it could make things worse — diverting the Sacramento River to Southern California. Management will matter.
3. DWR should not be put in charge of a conveyance because it’s a captive regulator — it claims to serve the people of California, but it actually serves water exporters who purchase water from DWR’s State Water Project. It would be better to either split DWR in two (SWP operator and water regulator) or have a regulated utility run the conveyance. Exporters could run it, assuming that they maintained environmental benchmarks. 
4. Delta communities and farmers are going to go. They cannot be protected from an earthquake/levee collapse/big gulp. If they are gone, the conveyance may allow the Delta to get as close to “natural” as possible — assuming that xx maf of water exports do not do crazy harm. OTOH, a conveyance will NOT end “shortages” in SoCal, since water is still too cheap and not traded there…
5. A few things I forgot?

Bottom Line: Many people are paying attention to the wrong issues with Delta conveyance. That means that they might “solve” the wrong ones and ignore the important ones.