First I wanted to say that I just saw that this was mentioned before but I think my idea is still different enough to be considered. Other than that I just wanted to say hi since I wasn’t active for a very very veeery long time.
so my idea is to have multiple weapons which you could switch between while playing. This could be done by having weapon slots or as I’d like to call them - weapon arsenal.
Before the mission starts you could pick the weapons you want to use from the weapons you bought.
you could switch between slots by using your mouse scroll wheel or by using the ‘z’ and ‘x’ keys.
whenever you pick up a weapon upgrade only your selected weapon will be upgraded.
Here’s a small example for what it could look like (it’s rough but better than imagining it :P).
This feature could become OP pretty quick so all ships will start with one slot, but in mid-tier ships you could upgrade it to 2 slots and in high-end ships you could have up to 3 slots. Of course, it won’t be cheap to upgrade - I think it should cost between 
750-1000 to have 2 slots and 1000-1500 to get it upgraded to 3 slots.
I think that this feature should be in the game for multiple reasons:
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It opens the door to more strategy - how should you divide the upgrades between your weapons? should you upgrade one type more? should you balance your your weapons? etc…
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It will incentivize players to play more of the game to get to more slots
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I don’t have any other way to say it - I just think it will be awesome
:D