it is possible to modify elo to make it a closer match to the luck element of pokemon.
it is possible to modify elo (using provisional ratings) to avoid players with inappropriately low ratings grinching lots of points at Nationals/Regionals.
It isn't possible to completely remove the play-at-risk factor that is at the heart of elo without abandoning elo. In an environment dominated by fast decks that just seem to get faster it isn't possible to make a good assesment of the risk. Elo is not appropriate and never can be for a game of solitaire where who you paly makes no impact on outcome. Solitaire play (T1 wins) is where an obsession with speed eventually leads and will result in many old hands leaving the game for other tcgs. I have no idea how important it is to pokemon's sales that it remains a game of skill.
2/3 helps but without draws can lead to problems with tournament scheduling.
I don't see the benched win condition going away.
Limiting elo to the swiss won't fix much
and by cutting down the information available to decide relative strength probably makes elo worse. Top cuts could have a smaller K value in the first round of the cut, and I'm sure that other modifications could be introduced to limit the impact of a first round loss in the top cut without wrecking elo. That double loss isn't any different to any other point in the tournament but players seem to be much more concerned that it can happen in R1 of the cut than at other points in the tournament.
A two-year ratings cycle helps, but would need care to avoid players being able to sit on high ratings.
It is not easy to design a pure-reward system that doesn't penalise players who are unable to travel a lot, don't live near a center of OP, or doesn't result in team play.