With that done, lets talk balance.
Teleporting
For me, the biggest issue FTL has is teleporting. For a small investment (75scrap), you can consistently capture ships - which has huge benefits - more scrap, more crew, and more weapons. It pays for itself very quickly.
You also don't need to invest in weapons (a bomb or missile to take out a medical bay/ reduce their firepower) is all you really need. Because weapons and weapons systems are so pricey, not having to do this lets you spend more on defenses, which means you take less damage, and get more money etc etc. It's also brilliant against the last boss. To put it simply, teleporting is reliable, predictable, and too good.
Raising the cost of the teleporter doesn't really fix this, because the problem is tied into FTL's biggest mechanical weakness - the boarding mechanics. For an example of perfect mechanics, look at the way fires work.
Even after 59 hours, when a fire breaks out on my ship (especially without the doors upgrade), it is dangerous, exciting, and just feels right. You think #$%*! my ships on fire, and try and contain the spread, watching systems crackle and burned crew flee to the medical bay. Boarding doesn't feel like that. Teleporting is 100% reliable, and once you get there it feels like you are playing a game and not boarding a ship/being boarded by a ship. Part of this is that the medical bay still works when intruders are there. This a) feels artificial, and b) makes the tactics simple. Unless you are by a sun or facing a ship which is already very dangerous, being boarded is nothing to worry about.
When you are the one doing the boarding, you don't have to worry about the med bay (because you know to shoot it), but you benefit from different weak mechanics. The combat is very predictable (damage over time instead of unexpected bursts), so you only risk losing someone to your own stupidity. Enemies can't obstruct your crew without reinforced doors, which few ships have. This lets you dance injured crew around with ease, particularly by using the pause function, which makes things even easier.
I have three suggestions which I think would improve this. The first is that the teleporter should have a miss chance, like missiles and bombs, and a chance of hitting the wrong target (equal to the miss chance). For example, you want to teleport your assault squad to the enemies weapons, but the enemy has an evade of 30%. This means there's a 30% chance the teleport misses (the crew just stay at home), and needs to recharge. There's a 30% chance it sends them to the wrong room (they teleport to a random room). There's a 40% chance they go just where you need.
The second is that medbays don't work when enemies are there. Simple and combined with suggestions 1 and 3 creates a new dynamic.
The third is that when a crew member is in the same room as an enemy crew member who isn't moving, they move at half speed. This allows crew to block or slow enemies, preventing too much dancing and getting free hits.
I think the result would make boarding a lot more exciting and fast paced. Ideally you want to get to their medicalbay, so they have no way to heal (or stop them getting to yours), but this will be quite risky without some softening up. It also creates the great situation of "target their engines!" "Enemy engines down! They're dead in the water" "Good, send the assault squad straight to their medbay."
The boss
I like the last boss - he's a nice challenge at the end of the game. But taken with the rest of the game, he creates a weird problem. The problem is because he's such a challenge compared to the rest of the game, you need to have a very good run to have to beat him. On most winning attempts, I get lucky/do well in the early sectors, and then can farm for the next 4-5 in relative safety. This was ok the first time, but not so afterwards.
In contrast to this, all my favourite games of FTL involve going from crisis to crisis, limping to a store, not being able to afford what I want because I'm spending so much on repairs, and each battle nearly being my last. But if you have a game like that, there's no chance at the end. This tension between the most enjoyable games, and winning the game seems strange, but I don't have solutions for this.
Crew
This kind of ties into the last point, in that if you are trying to prepare for the last boss, you shouldn't be buying crew - you can get a full complement by beating slave ships and boarding. Maybe they could be cheaper, or you could have a higher chance of finding your own race? I was sad to play the Zoltan ship and never get more than my starting crew as Zoltans.
There is a thread on this forum about veteran crew, which is awesome :
viewtopic.php?f=4&t=3553
To add to this, maybe we could buy crew who have some skill already? Or have extra crew able to give benefits to rooms like drone control and cloaking.
Missiles
Missiles are fine for enemies, but for players they're just much worse than bombs, because doing hull damage is way less important than disabling systems, so missiles aren't efficient.
Thanks for reading, and thanks for the game
The problem here is that later when you get your ship and crew in order it is very easy to defeat an invading army by running to the medbay. However before you get nicely sorted out, in the very beginning you are vulnerable to boarders esp. if you start with weak fighters. In order to benefit from the medbay's healing powers your crew must unmann their posts, which can mean taking on extra damage from the other ship's weapons.
