With Soartex I love the MPS suit textures, but with anything else (granted, that means Faithful or default) I hate hate hate them. They look so much fancier than everything else, it's so out of place.
Railcraft (and probably other mods, Railcraft is just on my mind right now) has a couple annoying recipes. I always end up building two blast furnaces (which actually ends up looking much cooler than just one alone) because the furnace takes 34 bricks but to build it I have to make at least 36. The same is true with strengthened glass. The recipe gives six, but the recipe for dyeing it requires eight.
I hate it when mods make you craft items/blocks with rarely used items, and you end up not using them anymore because they're basically useless. like nuggets, almost no recipes uses them, but the once that do only require a few of them, but you can't get yourself to throw away the ones you don't use, just for that one chance you might need them again
A great use for nuggets (in Thaumcraft 3, anyway, no idea if this is true or not for 4) is metallum aspects for research. One ingot will have at most 8 metallum, but each nugget will have 1 for a total of 9. Nice little bonus!
This one makes sense to me. Just like you need to milk snake venom to make an antidote, or culture a flu virus to make a vaccine. You need to breed the poisonous bees to learn how the poison works before you can make protection for it.
But the suit isn't protecting against the poison itself, it's protecting against the stings that deliver the poison.
This is annoying beyond belief except in one certain situation: I'm walking by the one house they all picked to stay in for the night. Then it sounds like I'm overhearing an orgy and it cracks me up.