Reach weapons use the ranged weapon rules for determining cover. Normally, Improved Precise Shot would get around this (at the cost of one feat and a useless-for-melee feat tax), but those feats specify that they only work for ranged weapons.
Are there any other abilities or rules that a reach weapon user might have to ignore the soft cover provided by allies between the reach weapon user and the target?
(Note: Teamwork feats and other solutions that require the ally to have a particular ability aren't much help here, as I have no opportunity to coordinate character creation/advancement with my allies.)
You might be out of luck if restricted to PF only.
In D&D 3E, the Precise Swing feat (requires BAB +6, nothing else, iirc) lets you ignore non-total cover with reach weapons.
Even better is the Goggles of Foefinding from Magic Item Compendium, which only cost around 2500 gp and let you ignore non-total cover for any attack.
In PF only, best option might sadly be to go into Ranger or Zen Archer Monk so you can get IPS at 6th level without wasting two feats, though along the way you'll waste class features and/or bonus feats going either route (especially as Zen Archer; I think as Ranger w/ Archery style the only waste is the 2nd level feat, as long as you ditch after 6th level).
Just talk to your GM about ignoring it completely. It doesn't add anything to the game, and what players can do so can enemies so it isn't actually a power boost.
It just means that Reach weapons can suddenly be used for what they were designed for.