More things! Yay! 
Yay, thanks for the interest
Checkpoints sound like a massive improvement on playability but this, of course, depends on whether a player prefers to play the game or compete with the game.
Yeah, at first I was fine without them, but the game is kind of slow paced, with lots of traveling, and doing that thing again and again after dying would quickly become tedious. The missions themselves are already structured in "parts" (that is, you get a batch of objectives, and after you complete them you get a new batch in a different part of the map), so having a checkpoint between each batch seems natural.
I've been thinking of adding a "Hard mode" after the game is completed, and this mode would disable checkpoints (while also disabling cutscenes and dialogue). That would be neat.
The fuel "burning" during dialogues could have been solved with a much more simple solution: pause the clock! 
This allows fuel to burn when hovering (as one would expect), for example, but keeps balanced whether or not one reads the dialogue.
By "pausing the clock" you mean like making it not burn fuel while a dialogue is up? If that's the case, then players who don't care about the dialogue will get the advantage of free movement while dialogue is up, and there's a LOT of dialogue.
I forgot to mention that dialogue popups don't pause the game, they don't behave like proper cutscenes on which you can't control your character and have to skip the dialogue with a button press. No, the popups just appear as you play and disappear after a few seconds. They serve as commentary by the kids that are playing the game, and for the most part is tongue-in-cheek and not critical to completing the mission.
I didn't want to make the dialogue interrupt the gameplay, so the player is always in control, and that's why I can't pause the clock. With that in mind, making it so you don't burn fuel while standing seems to me like the only solution: if you don't care about the dialogue, just ignore it and keep playing, but if you do, you are free to stop and read, you won't get penalized.
Secondaries charging by kills is an odd choice. You've already mentioned that they're a panic button (missiles/charge) or to be used in conjunction with the primary (missiles/freeze). Charging by kills means that once you've used it up, you have to be fine without it or you will die. Charging by time allows the ability to evade until the weapon is available where you can then engage properly.
If 15 seconds charge makes the game easy, increase the charge time! 
Yeah, even though the secondaries serve as a complement to the primary, you can still play fine with just the primary. The GIFs are kind of misleading, but in the real game you don't fight that many enemies at once, that would be a nightmare.
I played around a lot with the recharge timer, but I could never reach a proper "balance". If the timer is too short, you can abuse the hell out of the secondaries (which are VERY poweful), but if the timer is too long, you feel like you should save it for that special moment in the mission where you really need it, and end up only using it once, or maybe never (like the BFG9000 from Doom)
Also, people play differently. A fast, careless player that wants to complete each mission in under a minute would only have the chance to use the weapon once or twice, while a slow player will be rewarded unfairly with more uses. Playing slow is already safer as it is, so rewarding the slow player with even more charges would make this playstyle way too effective.
By recharging it by kills instead of time, it doesn't matter if you play fast or slow, you will only get roughly the same amount of uses. If anything, it makes playing fast more exciting, because you will recharge the secondary sooner.
Another option for secondaries appears with ammo. You can require a certain amount of ammo to use it or maybe have specific "charge" items to pick up.
For example, charge fully in 2 minutes, add 10% charge for each kill, and add 25% charge for each normal charge item picked up.
That way, you can have repeated usage with constant engagement (kills), begin engagement with a full charge (time and/or items) and have the option to build up that charge during evasion (items).
Thanks for the suggestion, although it seems a little complex. I would prefer using only one method to recharge, not a composite, just to keep things simple.
I didn't think about using an item to recharge, though, so thanks for that. However, using a item then makes the secondary be dependable of fuel (because, by finding the recharge item, you spend fuel on the way), so I'll have to add more fuel items to compensate. This brings the problem that if a player never uses the secondary, he will have a huge surplus of fuel. I guess that's a valid trade-off, but I need to think more about it.
The other option is to make the secondary share the ammo of the primary, with the secondary eating a huge chunk of ammo (say, half the bar), which would make the ammo management a little more in depth, but then again, you could only be able to use the secondary if you have more than half the bar, otherwise you are stuck with the primary, and this would force player to use the secondary, find ammo, use the secondary again, find ammo, and repeat and repeat, until eventually you don't have more ammo on the map, and suddenly the mission becomes unwinnable. While that's the player's fault, as the developer I need to minimize those situations.
Man, balancing gameplay is hard
I think Project threads are (or should be) exempt from this rule, particularly with posts from the creator. How else would updated information be shared? Another (newer) thread would be horrible, right?
I guess you are right. Still feels weird to post on a thread whose last reply was made 10 months ago, though.
Anyways, thanks for stopping by.
