In the current PvE system, players repeatedly clear the same sets of nodes and accumulate points over time. The Gauntlet format was a very welcome change from that. Here is another possible format to consider.
Each node awards a score based on some puzzle solving criteria. Every node has a different puzzle. It could be beat the enemies 20 turns to get 100 points; beat them in 15 turns to get 200 points. Or win with 80% health to get 50 points; win with 90% health to get 70 points and so on. Repeating the same node will not necessarily add to your score, but you take the best score out of all your attempts at that node. So players don’t need to grind it to farm points, but have the chance to repeat it if they think they can do better. Rubberbanding is not needed here since players who join the event late can still win, and it won’t make the early joiners feel like suckers.
The puzzles can and should be more interesting than just watching health or time/turns taken to win. How many crit tiles can you make. How fast can you get 30 team up AP. How many protect tiles can you create. What is the highest number of tiles matched in a single move. Or even what is the most damage you can sustain and still win (insert obligatory health pack conspiracy here). There are so many possibilities.
Some puzzles will strongly favour specific characters due to the nature of their abilities. This encourages players without those characters to obtain them through the cover packs, yet it does not lock anyone out of “essential” nodes.
There could even be bonus points for accomplishing certain tasks. Like turn Colossus invisible.
Maybe have colour challenges like cast Escape Plan on a board with no purple. Or keep Daken alive with no blue. Or opponents are A.Wolverine and Rocket+Groot, on a board with 50% higher chance of yellow.
edit: originally listed the wrong ability from Fury
edit: expanded title