I feel a little uncomfortable with mysterious scores which essentially say "buy this!". Kayak.com essentially has to lie to me to artifically raise an airline's ticket in the search results (at least, lie by omission), but SeatGeek seems like they could massage the rankings easily for a fee. I don't really have a reason to trust them more than, say, Yelp!, do I?
Certainly a fair question. I can pledge to you that we do not (and never will) alter our Deal Score based on fees or relationships with ticket sellers. Our team has spent countless hours building the components of this thing to make it hyper-useful, and it would be pretty awful for us if its integrity were compromised. But I realize that doesn't mean the calculation is transparent.
Beyond that, two things that may be worth considering:
1) Any inaccuracies with Deal Score are in plain sight. If a calculation is off and a ticket isn't given the Score it deserves, that's sitting out there in the open on our site. So it would still be easy for people to "call foul" if there were ever a problem.
2) You're welcome to ignore Deal Score and just sort by price. At that point you're effectively getting the same experience as Kayak. Deal Score is something we built to add additional utility.