I've tried playing Thaumcraft2 yesterday and i agree that some items like the Axe of the stream or the Sword of zephyr (i found them in chests, didnt have to research them) are being used up way too fast. I think you're supposed to have a Vis repairer to use them properly. Their durability would otherwise be too low for more than one expedition.
Also i agree that crystals are way hard to find, but i noticed that wisps are relatively common and fast respawning, and they drop crystals quite often, so now i go wisp hunting when i need crystals (the area where you find the wisp seems to influence the crystal type, for instance i found only vaporous crystals when hunting high above ground).
Wisps die easily from bows, but arrows are a pain to make (unless you have a chicken factory), so now i hunt them with boots of seven leagues and a sword. There's probably a better way to do it, like magic wands, but i'm still fairly new to the mod.
Oh and someone earlier said they were playing Thaumcraft2 on peaceful, and while i can understand (i do tend to play mods on peaceful now), i think this is one of the rare mods that you don't want to play on peaceful. Not only because of the brains, but many items and mechanisms have a strong interaction with mobs.