There's an excellent article in Computerworld on how IT portfolio management tools alone will not decide which projects get done. Politics, organizational dynamics, and subjective opinion still need to play a role, even with the best of software.
People have this picture in their mind that tools can be used to calculate ROI and magically align projects with strategic need according to a perfect formula. Voila! Automatic project prioritization and selection. The fact is that this is a myth. Tools can absolutely help, and can offer a first pass view of where projects line up. But ultimately, people must make decisions----and whenever people are involved, a myriad of other issues come up, including conflicts that must be resolved.
Here's the article at Computerworld, that rightfully talks about these tools as enablers and not the be-all, end-all ...
What IT portfolio management tools can't do: Stop politics - Computerworld