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?

The game is pretty hard even with easy difficulty. This kind of ship design cannot live long. At some point, you got to refuel your ship with scrapes, and the reliable way to get scrapes is winning a battle. In the mid-game, you may be able to run away from battle and looking for events to upgrade your ship freely or at low cost. Each jump consumes fuel, running into multiple uneventful location can hit you hard in a long run.

Also, we expect to face stronger enemies when advancing. Around the mid-game, you soon realize you need weapons to disable enemy shield, unless you have a transporter to beam a boarding party over there.
Burst Laser Mark II x 3 or Mark III x 1 could disable all shields.
Breach Bomb Mark I / II and teleport a bomb to the shield station and cause damage, reducing the need of Laser weapon. The same goes with missile, but you need the inventory, which means scrapes.
Beams are also an alternative way once the shield is down.

In a rouge game, you don't have much control on what sort of weapon and argumentation you can get.
However, I tend to reserve resources for the Cloaking. If I can't get it before facing the flag-ship, I would try to upgrade my weapon. It is because I believe offensive is the best defensive.

PS. They are referring to the standard edition. I haven't played the advanced edition yet.

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.