The following items have been seen to effect the speed at which Project Navigator opens
If a user is likely to open another project other than the project last opened before Project Navigator was closed, the "Always Open last Project" preference should be deselected. The preference can be found by selecting Edit -> Preferences and selecting "ISE General" in the Category pane.
The speed of a network may vary depending on load and connectivity. Generally, if the network is the issue, other applications will experience some delay as well.