A balance problem in this game is that modules are limited, while crew can go on increasing forever. I've had several ideas floating around:

One possibility is a new research tree or an extension of a current one. However, instead of better thrusters or dampeners or cannons, the research will open up a new type of module that you can have an additional 4 or 8 of. This way, additional decks have more use, upkeep can be rescaled so it isn't 4 times greater than on a Quasi, and people won't complain about their Voliir Bio-stabilizers going to waste.

Another possibility is an extremely rare NPC module drop that installs and then upgrades by a certain % each subsequent use, with no limit. This shouldn't be too OP in comparison to crew increases on large ships, and perhaps mining will gain another use if upkeep increases accordingly.

Finally, why are allies capped at rank 100? That's no fun. It's not too much of a bonus if they keep giving an extra +2 attack or defense each day. Although not sure what to do about upkeep, since you can't control leveling sometimes...