There's nothing wrong with the sign-in time priority system, per se. (In some cases, it's the only way I could have gotten to work in STL from Dallas.)
Changes I would like to see to the non-rev system in
my perfect world.
1. No changes to travel category within 48 hours of departure (i.e., people booking at D2, then changing it to D1 just because they don't want to have to get up at 2am to sign-in for a 6am departure. Or, they get up and see that they are way down the D2 list; so, they cancel their D2 reservation and put it back in as a D1.)
2. No booking of D1 travel period within 48 hours. If it's a family emergency, your supervisor can get you on the plane.
3. No signing in for a flight when you are at 36,000 ft. This is done all the time by flight attendants in two ways--having someone else log on as you and sign you in (a violation of corporate computer security policy) or having an amenable agent at your departure station sign you in once the 4 hour window is reached even though you are long gone. I've also seen a case where an LAS agent signed in an SLT flight attendant for their commuter flight as a through passenger (D2T)--even though that f/a was WORKING the flight from LAS to STL and just commuting to DFW from STL.
4. No booking on a flight that you cannot possibly make just so you will roll over on top of standby list for the flight you intended to catch anyway--i.e., booking 2 legs as separate reservations. First leg arrives at DFW at 0800, but second leg is scheduled to depart at 0745--or 0830 for that matter

. Technically, this not possible because agent is supposed to remove anyone from NRSA list who does not physically present themselves at the gate prior to departure. However, the agents are so understaffed and overworked these days that most of the time they just roll over to the next flight any names remaining on the standby list. And, yes I know that this will also get the people who had a flat tire/got stuck in traffic/etc on the way to the airport. But, how often does this really happen. And, if you live in a high traffic city, you should know better than to wait until the last minute to leave home.
Any of these changes could be easily programmed into the NRSA system. However, since none of the problems affect those people who get to travel pos space all the time, it probably won't get changed.
No system is perfect or fair to everyone, but deliberately breaking the rules just because you can't be bothered with signing in 4 hours in advance or taking your chances is just wrong.