I wish to add one seemingly innocent comment to the discussion:
More interesting weapons please.
I think the combat system we have now is paying the price for this lack of vision. I was very disappointed to find only a couple of energy weapons, projectiles, etc.
Referring back to my experiences in MOO2, it wasn't so much the strength of the weapons involved, rather the combination of weapons that made the difference.
The closest Stellaris comes to this is a combination of plasma and disruptors, where one weapon knocks down shields allowing the other to inflict more damage.
Make no mistake, I understand the game's designers are trying to avoid the all-powerful ship design that can't be matched. But, what I am saying is; rock--paper--scissors = meeah.
Simply making weapons more powerful by degrees is pretty standard stuff, but doesn't really alter the balance of power. In WW2 the tanks got bigger, and what was the result? Heavy tanks were resource hogs, too slow to keep up, inflexible in harsh terrain, and broke down with regularity. In the end, such monstrosities had no effect on the balance of power (Exhibit #1; Battle of Kursk).
In short, if this be a war game, then WHERE'S THE ARMS RACE?
Another example; in medieval times infantry got halberds, archers got long bows, cavalry got the over-run. Moving up the technology tree means one acquires new weapons and tactics (both offensive and defensive) that actually tip the scale of battle.
In Stellaris, simply stacking ships in increasing numbers and gradually boosting weapon strength by degrees is, well, meeah.
Now, ask yourself this; What's a better investment of research and resources:
a) gradual improvements, or
b) game-changing technology.
Remember too, the Huns bested the Roman legion with leaps in technology and tactics, they were not simply another barbarian doom stack.
I apologize for butting in, but MOO 2 really didn't have that much going for it in terms of combining weapons.
There were only 2 kinetics and they were just better versions of contemporary tech: Mass Divers were much better than fusion beams and could last until neutrons or even gravitons and Gauss cannons were better than phasors, contended with plasma.
After that it was straight up upgrading to Disruptors and king of guns - Maulers (which were plain OP and shouldn't have existed in the first place).
Special weapons were indeed interesting: all those tractor beams, plasma webs, the iconic stellar converter (destroying planets really sped up cleaning up the galaxy) or even the vaunted Black Hole generator,
BUT, in terms of effectiveness to space taken they were much inferior to just more simple guns.
Missiles were only efficient in the early game were missile cruisers were highly efficient hit and runners, but even with mid tech they were easily countered by equipment or even simpler - more guns.
Torpedoes suffered from both lack of damage and 2 turn delay between attacks. Fighters and their upgrades were famously underpowered and could be shot down by basic guns as well.
What was actually interesting is all the little modifiers that the game had, like direction of the guns mount (sadly not applicable in Stellaris as all guns are 360 turrets) and heavy (think of them as L weapons), point defense (respectively S weapons),auto-fire, continuous, armor piercing, shield piercing and enveloping.
These features in Stellaris are sadly in-built into weapon types themselves.
However, your statement holds a kernel of truth: space combat and ships should be more interesting. So far damaged ships will be getting mounting combat penalty, but i would really like if more parameters were tracked and there was a chance for a critical hit and in the best case (or worst, depending who is on the receiving end) a reactor core breach could happen causing the ship to go total kaput or maybe a gun would be disabled for a short time. AoE damage of sorts could be added in. The AoE most likely would have to be small, but respectively gravity weapons that would bunch up ships could be used to help with that.
Sometimes, i feel that Stellaris suffers from a lack of ambition instead of being overly ambitious, especially when I take a look at the deeper mechanics. Hopefully Wiz and others at Paradox will take a long critical look during the development of 2.0.