Sounds very similar to Endless Sky[1] - another open source game drawing on the old Escape Velocity games. I really enjoyed both Endless Sky and the Escape Velocity games, so I'll have to check out Naev at some point!
My one combat was decidedly one sided and a disaster. I honestly don’t remember the game play of it much. Most of the navigation and movement is automated.
By the time I got enough money for another ship, I had become disenchanted with the mechanics. Trying to min/max sales and trade and such. And was never strong enough to play Galactic Marshal or anything like that.
That’s when I put it down. Just may be the game doesn’t suit me. Or I never got into some sweet spot of challenge to engage me. And since the galaxy is fixed (at least I think it’s fixed), I didn’t see much opportunity in replay of it.
(And that's before you discover [censored] and [censored] and the whole [censored] storyline that happens after the “main”/initial plot ends)
Some brief notes about combat in Endless Sky (with some differences from EV:N):
* The population of ships is much higher in ES; it's much easier to get overwhelmed. Note that when you initially enter a system it starts with 5 seconds (I think) worth of ships, and they keep randomly spawning at a continuous rate (in the game files, the numbers mean "expected delay between spawns in milliseconds" I think). If there is a hostile enemy ship, chances are its random delay was pretty short, so more will come. Instead you should try to arrange your fights to be in a system with low traffic.
* The easiest way to get started with combat is to take escort missions, which spawn fixed enemies, and have allies that you can use as shields. They also persist if you disable them and land, so you can capture them easily (sell your fighter and buy a shuttle which can hire more crew). This is by far the fastest way to make money (as in, pay off your debt on day 3).
* Ships do persist between systems, so if they jump out you can follow them
* You absolutely can play the game without ever buying anything or doing missions, slowing capturing more powerful ships until you get a Bastion. This isn't a reasonable thing to do, but I did it anyway just to prove it can be done.
* The Monty Python maneuver has been heavily nerfed, but still has an important place.
* There are 4 different approaches for weapons on your ship/fleet; each ship should largely pick one and stick to it (and you should ground ships with the wrong loadout for your current task): 1. do as much damage as possible, 2. reliably stop shooting when target is disabled (that is, beam or weapons or at least high-velocity ones (though this is less important against slow and tanky enemies); it won't help if your allies see another target behind it), 3. overload enemy heatsinks (very useful against certain ships but useless against others), and 4. drain enemy energy (I've never found this useful, but have been affected by enemies using it on me). Also a couple special cases: 5. the player ship should be somewhat optimized for capturing, which may be at the cost of weapons, 6. your main ship might also want extra fuel, for exploring or just avoiding deadlines (escorts can land/takeoff to refuel without taking an extra day ... they can share with you, but they are dumb if multiple uninhabited systems exist on your path), 7. anti-missile also takes away from direct damage but is usually worth it (and without the tough energy/heat costs), 8. it does matter which gun slot you put your weapons in; use the I(nfo) window, 9. weapons that use ammo get expensive for the player's fleet, unlike enemy ships (and I guess mission-based escort ships, but those are rarely really combat-capable) which get everything for free; unlike EV:N your permanent escorts don't refill for free (but you do get to choose their loadout, so it's a net win I guess).
* Regarding engines, steering is generally more important than thrust for both combat and escaping to another system, but thrust matters for escaping/dodging within a system. A full guide to optimizing your ship would not fit in this margin, but it is certainly possible to beat the default ships, especially by mixing outfits between factions.
* Many factions will forgive you easily if you just attack pirates or something, but some factions will never forgive you. If you accidentally draw aggro merely jumping between systems should suffice.
* There are some outfits that you can only get by boarding or capturing a ship, and some that you can only get by capturing the whole ship. This includes outfits never buyable, outfits only be unlocked later in the main plot, and (if you use 0.9.8 which is still widely deployed) outfits that were supposed to be removed for balance reasons.
I was having a blast being an explorer in a scout ship, shuttling interesting characters around, never getting into any battles because my ship was fast enough to outrun any pirates and I never pissed anyone off.
Unfortunately at a certain point the game the railroads you into a storyline where you are forced to pick a side in some galactic war and entire sections of the map become unpassable because everyone attacks you, even if you are pootling along in a civilian ship with no weapons. I think you're supposed to build up a fleet and kill everybody, but it's such a big change in both tone and gameplay that it really bummed me out. Oh well.
Note that none of this involves the storyline, so you can do this for as long as you'd like regardless of how much of the story you have completed.
I wonder if the Coalition campaign is done yet...