Neat little game. Got a good thing going with swapping out to a Burst weapon and upgrading it a lot, and I basically steamrolled out to Sector 18 before it was clear that nothing was left that could pose any challenge. Homing and splitter paired with a powerful weapon that vomits all its attacks immediately, all enemies up to and including bosses just kind of melt before they can do anything. With even bosses dying before they can summon any minions, there's no challenge left. I even had the avoid death perk on an item, not that I wound up needing it.
For that reason, weapon upgrades seem seriously undercosted. They're the only thing you can buy that scales indefinitely, and they're reasonably cheap to buy. This makes service shops the most valuable destinations, since they're where you get that amazing benefit. Tier upgrades are sort of okay, and you should max out enough to get by, but what you really want every time is to turn your weapon into the all-slayer.
Despite being all-in on Burst, I didn't have the opportunity to get the Burst specific skill, since I'd have needed to pick up eight levels of weapon skills that I wouldn't be able to use, at a cost that had already become very large. That felt pretty bad. I think all the weapon specialisations should branch off a single point, so you aren't penalising players who want to get them with a ton of dead levels.
It took me a while to even notice that you claimed missions by clicking on them, which was a bit of a waste of time very early on. Once I figured that out, death was still frequent enough that missions were something to save for the start of a new life. Later on, missions were useless because I already had all my slots full so I didn't care about another Tier 3 loot drop and I wasn't likely to die any time soon. That said, it felt like the anti-elite mission (and Elite POIs in general) shouldn't appear in Sector 1 (I foolishly took one early on since it had a better reward, but it wasn't doable and couldn't be dropped). I actually killed my first boss before I managed to deal with an Elite POI; having to deal with a bunch of enemies at once is actually harder than just one powerful enemy and streaming reinforcements.
Also, I kind of wish that modules with more sockets appeared more often, perhaps available in shops at a higher price. Past a certain point in the game I'd absolutely trade a tier 5 module with one filled socket for a tier 1 module with three empty ones, but I'm not often given that kind of opportunity. Rare ways to add sockets would also be nice.
Noting that prestige is currently disabled as per the devlog, I'd suggest that the obvious prestige mechanic is to swap out for a better ship? Higher base stats, more slots, a different starting weapon. Maybe, instead of just buying your preferred options off a menu, you shop from a store that gives you a limited variety of randomized ship choices, and the further you got, the more likely you are to have access to higher value ships?