There is no reason to pick Phase Run over Comet or Summon Aerie and I'll tell you why....

To stat the obvious, you miss out on the damage from Comet and aerie, but its doesn't end there. Phase Run usefulness is highly conditional based on your opponent.

Let me explain.

1-The slow resist can only become useful if the target has a slow to begin with. If you  are fighting Yasuo in lane,  you get no benefit from the slow resist. 

2- You actually have to get hit by a slow, to get slowed. Sometimes your opponent may just plain miss their slow ability or you may just juke/outplay it.

3- The movespeed buff is only usefull if you actually move. If your target just plain stands still while fighting you, you get no benefit from the movespeed.

4- The movespeed bonus is really low when compared to Fleet foot at 15-40% movespeed when compared to 30% from feetfoot. Even if fleet foot move speed is only 1 second, it is way easier to proc and predictable. Not to mention it starts at 30% movespeed while phase run starts at 15%. 

5- At 400 or more move speed, you get depreciated returns  as move speed caps kick in at 400 and 500 move speed. Kinda like armor and magic resist. If it were more like lethal tempo and remove the movespeed cap then it would be a different story, but it is not.

The point I'm making here is, Phase run is kinda hard to proc and the benefits are very situational. Sometimes you may get absolute no benefit from procing the keystone because you have to get hit by a slow first and foremost, then you need to actually be moving in the fight to gain from the move speed.

Now after all that, you just gave up actual damage runes for something that is very situational.