Hmm... a few good points. The liquid boiler thing wasn't a nerf specifically. It was a change to the math of how it heats and produces steam. But it did render it far more inefficient. I only ever used one as a power system in 1.4.7. Lava stone is a big reason not to use it, I agree.
Powered Rails. Right. You can send one cart at a time. With a train, you can send ten. You cannot move fluids with vanilla rails. Nor can you send them along more than one path. You have to build several entire rail lines if you want to move items to more than one destination, instead of one line branched off to others. And even with the vanilla rail trick, it's still only if they're in the same order each time. Can't say Custom Named Cart 1 goes off here, Cart 2 here, Cart 3 straight.
Fair enough. I admit this one was outdated even before it arrived.
I have never used High-Speed Rails. I can't imagine why anyone would want to. If you want to go fast, you throw on more locomotives. Nearly as fast, and anything on the tracks gets splattered, instead of blowing up very expensive rails. If I need more speed, I lay down reinforced rails which already have a speed boost on them, and don't require transitions.
Trains can be self-loading, with no more than the addition of an anchor cart. And now it only keeps the area around the train itself loaded as it's moving. And yes, they do take Ender Pearls by default, but could be set to accept anything by tweaking the configs. It's done to keep people from over using them on servers, not that anyone uses those over free to use Chicken Chunks/Dimensional Anchors. And if they do, it's because they've set up an enderman farm so they're eternally powered anyway.
No, Teleportation is simply the ultimate expression of the issue. Carts of all kinds were rendered completely useless the moment Buildcraft first let us plug two pipes together. I can't see your issue with the crafting system. It's no worse than sitting and waiting on Mekanism's Infuser to process redstone into compressed so you get more than one circuit for it.