There are no real disadvantages that I know of.
In fact, the three desktop computers which I use on a regular basis all have PCI IDE controllers.
However, I have noticed a strange performance issue on a couple of old Win98 PCs (Daewoo CB649M-SI motherboards) where the CD drives wouldn't operate at maximum speed if they were connected to the motherboard and the hard drive was attached to a PCI IDE card. I tried installing WinXP on one of these PCs, though, and the problem went away. This problem doesn't occur on my main PC, a two-year-old Athlon 1.2GHz with WinXP. I doubt you will see anything like this; I've never heard of anything like it before (and, apparently, neither had the e-mail technical support department of the company from which I purchased one of these PCI IDE cards).