Commanders can select a phasegate, and it will have a "Primary" toggleable state. When it is set as "Primary" all phasegates teleport to it first, it is now the default destination. When using the primary phasegate, you get teleported to the next one in build order, at which you have a 5 second grace period to go into that phasegate to a new location, and so fourth until you stay outside one longer than the grace period. This grace period is to prevent simply looping back to the primary phasegate. (If people would get comfortable with the menu system I outline below, this will be redundant as they will simply choose their destinations all the time, but for new/lazy players it still allows the traditional method of cycling through them.)
Marines have a button (maybe the use key, if you hold it in open space with no interactive objects in front of you, it pops up a radial menu whose elements are the phase gate locations. When the "wheel" pops up, the primary pg is a different color to let players know the default destination (for teleportation from any non-primary phasegate), and using the mouse, the marine can select a new location which is prioritized once over the primary one when you next use a phasegate (if the commander designates a new primary phasegate in that time it will supersede your previous pick though). At teleportation the user destination resets and you have to repeat the process (via the menu) if you want to go to a specific location again. The mouse menu phase gate location elements are also shown in a map preset order, so this menu displays the phasegate locations in the same way always so it becomes an intuitive interface as you naturally learn it (can base phase gate radial menu location bases on actual map locations from a some central default point). I believe this new functionality will fit right into the game and will be very easy and quick to use, and you can use it easily while moving (While running for example. This menu still allows all ingame interaction with exception of mouse control. Prep a menu and walking into a structure to build it is another example.).
I'd also like phasegate armor to be displayed, and for the menu elements to flash red as a phasegate may take damage in real time. This allows marines more map awareness, but these features might just be clutter information.