Not sure about this, but here goes:
Allegiant may (I'm not sure they really do or don't) have more brake issues because they are based in Las Vegas, with a field elevation of 2100 feet above sea level, and high ambient temperatures through the summer months. Approach true airspeeds are a little higher there, and given the placement of the taxiways for exiting the runways there, some guys are temped to use brakes a little harder or earlier than they should. Don't know if any or all of their airplanes are equiped with brake temp indicators, but they should be. It gives guys a much better idea of what sort of braking energy they're really using. You need to be fairly late in the landing rollout before applying brakes on an 80...ideally say 115 knots or less...(that's not always possible or prudent), or you're going to heat up the brakes. Some 80s had bigger brakes than others, ususally as a function of the max gross weight. It can help to remember which brakes you have, and only apply heavier braking if needed on the bigger brakes. Even with the brake temp indicators...a crew who uses the brakes hard can get off the airplane before the temp indicators can show the peak temps...it takes about 12 to 18 minutes to max out because the temp sensors are not mounted right at the hottest part...the heat has to be conducted through adjacent metal before it gets to the sensor, and this takes time. It's not unusuall for a new crew to come aboard and find the brake temps high, driven by the use of premature or heavy application of brakes by the inbound crew.
If the company maintenance folks are tracking landings per brake, they can compare that to industry averages, and flight ops can then determine if any changes need to be made to recommended procedures or training. Then again, one has to wonder about the brake shop too....
One other thought...are Allegiant airplanes equipped with auto brakes...and are they routinely used? If so, that will cause heavy brake wear and high brake temps....even at the "minimum" setting, because braking is applied at high speed.