So, I've played FTL a few times on and off over the past few years. I really like the general design and want to like it, but I have come to the conclusion that I just really, really dislike like the design of the flagship. I'm curious to hear what some other players' thoughts are on it.

I don't think it's just that the flagship is stupidly powerful (which it is - I admit I haven't ever managed to beat it). I'm fine with tough games, tough bosses etc. I've beaten some pretty tough games (e.g. Castlevania 1, Super Ghouls & Ghosts). I just really dislike it on a fundamental design level, because it seems to undermine the freeform, roguelike nature of the game (which is otherwise great).

It seems to detract from the roguelike nature of the game, to have this extremely powerful, fixed end boss as a final challenge. It's so powerful that it seems to completely dominate over the rest of the game. Once you realize how powerful it is, the whole nature of the game seems to suddenly change from being able to freely develop your ship how you want to, to having to develop it to beat the flagship. And that seems to quite strongly restrict the player, because only a subset of the available weapons and strategies seem to be effective against the flagship, which renders a whole bunch of possible build options totally useless. For example, the flagship is clearly a slap in the face to anyone who wanted to go for a fast, evasive type of ship design, that would dodge and run, rather than sit and fight.

I just don't like the feeling of being shown this nice variety of directions I could go with my ship build, but, in reality, it comes down to: "we're just going to slap you in the face right at the end of the game, if you didn't kit out your ship in a very specific way to beat our big cheating monstrosity."

Perhaps I'm looking at it/thinking about it the 'wrong way' and I'd like to hear other peoples' points of view on it. Also, are there any good mods available for the game, that take out the flagship, or change it to make it less powerful, but also less predictable?

Ok, but it still could have been part of a more viable strategy. Perhaps not trying to run away from every encounter, but from some of the tougher ones, or those that your ship isn't well-suited to take on. But, the design of the flagship seems to completely veto even partly using such a strategy, since any resources put into making your ship better equipped to evade and flee are essentially wasted.

And that's part of what annoys me: the game includes build options that are clearly intended for building a fast, evasive ship, but the flagship completely neutralizes that possible strategy.

So, what are your thoughts on the flagship? Do you not think that it being so powerful detracts from the rest of the game, to the point that the whole game basically becomes 'about the flagship'? Basically, beating the flagship is the game - the rest of it doesn't really matter.

Factors related to evasive I can think of are:
1. Engine level
2. Upgraded Piloting sub-system
3. Cloaking device
4. Crew skill level in Engine room and helm

Option 1: An upgraded engine without power is useless. So you need to invest in Reactor as well.
Option 2: It increases the evasion rate without drawing power from the reactor. Nice to have, but not necessary.
Option 3: It is the best evasive system in the game. It is possible to push the evasive rate over 100%, thus not "essentially wasted".
Option 4: Crew skilled in engine station at engine room, also skill in piloting station at helm increase the evasive rate. It will come naturally along the journey. However, it is best to manually train your crew in early sector, when the enemy cannot hurt you in battle.

In terms of "fast" ship, I don't see any.
While there are arguments can shorten the cooldown time between jumps, it only works in battle. Unlike any starship we saw in movies or TVs, our ship in battle cannot "move behind the enemy" and start firing.

I think you are misled by the introduction, which asking you to delivery a message to sector 8. I was misled as well.
However, reaching sector 8 is not easy in itself. It took me about 10 attempts to do that.

Beating the flagship is the game indeed. However, imagine yourself as an explorer, explore every event is fun too.

I do feel like the game is misleading. The game that is presented to the player initially (freeform, randomized roguelike) isn't what it's actually about (beating a very powerful, static end boss).

I can't help but wish they had broken up the flagship challenge and spread it more evenly over the rest of the game. It would have made for a better game, imo.

I hate it as well...... in fact the entire game....... just I.M.P.O.S.S.I.B.R to the U!

Why do they make these games so stupidy unfair?

I wouldn't mind if each run through leaves you with some small buff to make next time 1% easier..... it doesn't. What few "achievements" you have are also IMPOSSIBRU and have almost NO benefit whatsoever.

Time to rage quit this turd.

Be fair.
It is hard, but not impossible.

I just managed to beat the game for the first time in playing about 30-40 hours an easy.

And here is how I did it:

I had a 2 heavy Ion cannons (3 energy each)
A crew control device
A simple laser (1 energy)
Drone control with 2 drowns Attack and Defense both 2 energy.

During the run through, I used the Ion cannons to disable shields and their weapons
And then later hammer their O2 systems till the crew dies having no O2.

Sometimes finishing them off with a simple attack drone or later a laser. When they would do too much hull damage.

This saved a lot of resources, because I seldom got hit and had no need to buy missiles.
And used only few drown parts.

The 3 end battles with the flagship were actually easy. You get different versions of it. The most difficult one to beat was the one with 3 attack drones.

I always thought ion cannons were trash because they do not destroy the enemy hull.
But men was I wrong: They actually are top tear.

I think there are a lot of different strategies to try to win. But this one works.
The only problem may be the start to the point where you can get the second ion cannon. Because it takes a lot of ressources to upgrade attack control early on and you to balance defense a bid.

And I only tried this, because there was a achievement that requires 2 systems disabled by ion cannons. But you can only get to 3 systems at best with one of them. And when I played on, it was very easy.

I grabbed a couple from Nexus, IIRC, including a save-game that allows you to keep more than one save and reload it, like a normal game save. The only one I have used was one that adds some extra loot and scrap for the later levels. I have beaten the flagship final boss. (Twice; there is a second fight with it immediately after you beat it the first time. You have to chase it and fight a damaged version of it again.) I had beaten the earlier version more times, since they made this latest version much, much harder than the earlier ones.
My strategy was redundancy. I had a transporter and three mean fighters (a couple of mantis and a rock) with a full drone system, some cloak and good shields with pretty good weapons — including an Ion gun.
I lost two of my fighters on board the ship when it jumped away, after I beat it, and they were gone for good. (I was not happy that I just missed teleporting them back.)

My understanding of those alternate ship builds is that they are there mostly to teach the player about the various competitions in the game: Dodge versus Missile, Cloak versus Laser, speed versus resilience, etc. (I think the game is reactive, too; by that I mean I think it will give you loot depending on what your game needs, so that if you are trying to do a stealth run to the fifth system it will give you more abandoned scrap to collect without a fight, for instance.)
So, whilst your point is valid, it doesn’t change the game that much, since you have to design a ship to beat the mooks, anyway.