Are bombers the ultimate weapon?

While there are many powerful turrets, in my experience the game is heavily biased toward carrier ships, especially multi-hangar classes. If you have a fleet of 3 x 2 hangar ships, with a well upgraded (max numbers + range and burst) mix of missile/plasma bombers (I usually do a 4/2 ratio) and basic PD (say two upgraded bolters a piece), and you zone in at a distance from the enemy, you can essentially steamroll anything. You might as well have no main weapons (though if you just use Projectile Cannons your ships are nearly untouchable). The fighters themselves stop nearly all incoming fire either (a) by absorption or (b) smothering with the massive amount of projectiles. Coupled with the fact that they quickly replenish (at no resource cost) and are fast enough to catch anything, no other setup really compares.
- Pure long range is very difficult, as you basically sacrifice any real missile/fighter defense, plus if you are outnumber they will snipe you first!
- A heavily protected close ranged armed option is also not really viable, because you chase the enemy around the whole map while they whittle you away with a damn Projectile Canon, since their are no speed upgrades. Both situations exacerbated by the g-d d-mn shield ignoring missles (in what Newtonian universe does that make sense?).

Essentially on hard mode, especially later maps, there's only one decent option.

Anyone else have similar experiences?

Winning with carriers is certainly one option. i agree that for much of the game, you do steamroll everyone. I'm surprised you have luck with missle bombers though, plasmas always work way better for me. The major downside I see with a fighter-heavy approach is that carriers tend to be relatively weak hull-wise,which means that if a fleet of alien capital ships jumps right on top of you (which they have a habit of doing), you're toast. This has happened to me more times than I care to recount.

I've actually found that my most successful games/highest scores are those where I focus on my onboard weapons and use repair/shield drones exclusively. Once you get 3+ death rays, it really doesn't matter what else you have.

I'll take a load out of Projectile Cannons and repair drones any day. In my experience, this is the most dominant load out. Not only will it crush your hull and swarm your fighters, it can easily bring your shields down too. If you think of it from a PvP standpoint (which would be an amazing feature btw), this fleet would shred you to pieces. Also, like @Forty In Red, my best runs were with repair drones and I've had a lot of runs where flaks or heavy missles drop on top of me and I'm toast. Fighters don't respond as fast as projectiles.

I'll have to try to complete a run with missile bombers tho. I haven't had much luck using them.

Agreed with above, by far my best Hard runs (as well as my first ones) were with me flying a heavy gun ship and carriers just as support (although contrary to above I did use upgraded missile boats and find them very effective, but by end game primary dps/alpha was beams/megaplasma by far so I should have probably just swapped to repair but couldn't even be arsed since I was in no danger anyway with proper positioning).

An additional issue with heavily fighter-dependent DPS is it dramatically increases the risk, particularly early game, of bad rolls in terms of environmental hazard systems. You can be going along and find a blackhole choke point, and suddenly your fighters are all popping before they can even make it to the enemy. Something a capital with some decent primary weapons could muscle through fine becomes grueling, particularly if/when there are no stations nearby and a constant stream of reinforcements. Even asteroid systems can be an issue if you've got bad luck.

And of course, fighters can often be really, really stupid and die barely doing anything but blocking some shots.

So ultimately I can see how a max count of upgraded ones could ultimately overwhelm a lot of this, but it seems like they're fundamentally just less reliable overall, and if you build your fleet around them then a bad fight could go really bad. It's game over if your ship dies really, I've never found an escape pod to be even remotely worth the loss of an entire weapon slot, particularly because by the end the loss of your primary ship represents an immense destruction of scrap/upgrade resources/lucky weapon finds over the course of the game that pretty much is impossible to reasonably replace, so you're toast anyway. Better to just not die at all.

Trying a max bomber run sounds like a fun challenge though and variation.