First complaint, L2/R2 ...
XInput handles triggers as a
single Z axis, this is problematic with all kind of
Direct Input games. is not the game's fault for being made before the advent of XInput, that is like blaming someone of being born. some games have no problems mapping axises to button actions but even on those cases you can't use L2 and R2 at the same time because they cancel each other, simple test: go to control panel and open the gamepad settings, press L2 every is fine right??, now press R2 without letting go of L2 and will be the same as if you pressed nothing.
a game that act like that?? NFS Underground 2 is a prime example of this behavior, support gamepads but was released before XInput.
another games that are better suited with the D-Pad don't recognize it because the D-Pad is mapped to POV, here I can say that is bad gamepad support for part of the game, but just by complaining the game isn't going to magically work with the D-Pad, in those cases I map the D-Pad to the respective X and Y axis and everything works like a charm.
of course any of this is SCP fault, but the only way around it is MotionInJoy and/or BetterDS3. SCP is a XInput wrapper, and as such does the job well.
DS4Tool is different and I love it, does almost anything right, just the last version went to shit again not letting me map the touchpad button as xinput back button but I'll stick to the previous version until they fix that and add Sixaxis support. with DS4 there is no much trouble as the control itself is properly recognized without custom drivers and L2 and R2 are mapped as separate axis and buttons, the only thing left to do was XInput, touchpad support which is exactly what DS4Tool does and Sixaxis which is being implemented.
my complaints are about SCP inability to do so with the Dualshock 3.
Edit: BTW I'm using this DS4Tool:
http://dsdcs.com/portfolio/software-development/4-ds4windows