Availability. Local availability can be hit-or-miss. The manufacturer that the local big box considers its darling this year might not be the same months or years down the line. This feeds into the compatibility issue above.

Initial cost. Crimpers and expanders (depending on which PEX solution you go with) are more expensive than a torch, flux, and solder.

Support. If things get hairy and you have to get a professional in, it might be harder to track one down who is familiar with the PEX manufacturer you chose.

Tasty goodness. Mice can't chew through copper.

That being said, I redid my house completely with Wirsbo PEX. Nothing but love for it.

I ran across some inexpensive leak detectors last year, one of which I placed under the kitchen sink where it warned me of the early stage of a sprayer hose leak. I highly recommend these in places where leaks might occur such as water heaters, washing machines, toilets, and other sink areas. Lowes has these @ $13 each but I stumbled across them on sale for $6 at a local discount store. One 9-volt battery supposed to last 5 years.