I agree the perception looks bad on TV and in person when you can see 40,000 bright yellow seats at Heinz Field, but not all of those empty seats are unsold tickets. I attend many of the Steeler games as well, and you will see thousands of empty yellow seats for a sold out playoff game, because the standing room on the rotundas and near the endzones provides a much better view than the upper deck. This is true of many pro stadiums that would prefer you stand with a beer in your hand near some railing, as opposed to sitting in your seat. Traditional bowl or sideline style stadiums that do not have thousands and thousands of standing areas always look more full because people remain in their seats.
I think a stadium of 50/55k would be reasonable for Uconn if you are only looking to expand the Rent. I think the 65k stadium Pitt plays in is just too big for most games on the schedule, as I much prefered when Pitt played at Pitt Stadium (40k) and only played PSU, WVU, and ND at Three River Stadium (60k+). But if you only are going to have one stadium, then larger is better for the few big games you have each year. Uconn's football time in the Big East did not allow it to show its stadium filling potential. With Uconn in the ACC or B1G having BC/Cuse or Rutgers/PSU as rivals and home games against the likes of Clemson/FSU/UNC or Mich,OSU/etc, the 50/55k stadium you proposed would easily sell out for many games. Although, if Uconn football (including the opponents fan base) can capture shares of the NYC market, you may find that a 65/70k seat stadium only selling out 2/3 games a year is desirable.
As for worrying about stadium attendance for FCS opponents, well those are only on local TV so it really doesn't matter. The games worthy of real national TV (ABC, CBS, ESPN) in national time slots (Saturdays at 3:30 or 8) that are actually being watched by most of the nation will easily sell out a larger stadium and create a better atmosphere for the game and on TV.
And I won't knock BC for not traveling to ACC games, as they would have a 1000 mile commute to attend any ACC games prior to this season. I suspect they would travel just fine to see Cuse and Uconn.