Outside of the true 3 point system which to me is clearly the best system possible, I guess something else that could be worth considering would be removing loser points and only giving 1 point to the winner for a SO win instead of 2 points.
In any case, the current system is very nonsensical(some games awarding 3, some 2 points) and creates fake parity. I assume GMs like it for job security because they can just say "look we're only 4 points off a playoff spot" but that just has the consequence of making the trade deadline boring because everyone thinks they're "in it".
A true 3 point system would be far more indicative of how good the teams actually are and would make for more exciting and interesting trade deadlines.
Another thing is that a 3 point system would actually encourage teams to win in regulation. Right now, if we are in a tied game with 5 minutes left, both teams are very likely to just sit back, take no risks, and try to get the guaranteed point. Why wouldn't they? There's really no penalty in doing so. With a 3 point system, the teams would still have something to play for during regulation, as that's the only time they could get 3 points. That might lead into more exciting and offensive gameplay towards the end of regulation.
All in all, a 3 point system would in my opinion improve the game in various ways, in addition to being more fair and making more sense.