Any BSD will have worse hardware support for the most part; and things Flash or other software that has no specific BSD port will have to be run via a Linux emulation layer, which may affect performance a bit. (I thought I'd read something recently about Gnome ditching BSD support.)
As far as I understand it, the .pbi installation files for PC-BSD work like Mac's .app directories: all of the requisite dependencies and libraries are included in the install directory. This equates to much more disk usage for applications but mitigates against conflicts. .deb packages do *not* have that capacity. Debian-based package managers usually handle dependencies extremely well, though.