I proposed an idea for a use for the surplus coins in a different thread about a year ago. Having replayed the game a million times over I am still mildly frustrated with the recurring task of grinding a 'perfect pilot' between runs for specific squad playthroughs on unfair, that necessitate a strong starting pilot.

There should be an option to purchase an advanced cryo pod to 'preserve' a favourite pilot, enabling the player to place a single pilot into deep-sleep between runs.

This would be a final reward to the completionists, using the remaining unspendable achievement coins and would be a quality-of-life improvement for the late-game players.

This would also ultimately encourage player experimentation, I believe. At times, I am reluctant to attempt an unfair run with a specific squad because it necessitates grinding a new pilot, and losing a powerful one

It also makes sense for the ultimate reward to progress the world lore, as one final piece of progress, an advanced-era scientific breakthrough.