You mean the reasons not to like GregTech? Mostly because it slows down the game.
The real issue people have with GregTech is that it delays damn near everything "endgame" and even some things people don't consider "endgame" even if they really are.
For example, BC quarries. That's a endgame item actually, as it gathers way more resources then the user can, and does so much faster(well, can anyway, assuming it gets enough power). Yes, it doesn't mine specific blocks. That's in some ways better as it will provide the player with large amounts of building supplies or scrap fodder.
Quantum Armor is obviously end game. That's kind of the point of it. And the only real block between people and their Q-Suits was a mass fab. Considering how powerful the Q-Suit is, I always thought that it was too easy to get.(set up a good nuclear reactor and make sure you have tons of scrap and you'll be swimming in UUM in no time) Now you need to mine several blocks of iridium to be able to make a matter fabricator, and there is 1 block of iridium every five chunks. Roughly.
So this has lead to players just using the quarry and strip mining massive swaths of land to get enough iridium to get their Q-Suits, which bugs my "don't despoil the land needlessly" mindset in Minecraft. Well, I have been known to set forest on fire with a wrath igniter so I can find my way out of them. But I ignite the leaves when I do this, mostly because the leaves are better connected.
Some people might be saying "But the Macerator requires DIAMONDS now!" And yeah, it does. If you don't strip mine and instead just cave a bit while you search for tin you'll likely find diamonds as well(even more so if you have only IC2 tin enabled which is deeper in the earth then other mods). Plus diamonds aren't all that rare or expensive.(IRL the only reason diamonds cost as much as they do is because various diamond companies jacked the price and and if you sell below their set value they will send assassins after you)
Now if the macerator required steel I'd be a bit upset because it's harder to get steel in GT then just railcraft or UE. Still possible, just harder. But diamonds? I can find those in any biome, and in any worldgen from vanilla that has chests. There are even diamonds in chests from TC3(barrows).
I mean, it seemed really odd to me that the macerator required flint but you never needed to replace that flint. Flint isn't very sharp, nor tough, so I always thought that was kind of dumb.
Tl;Dr Greg makes people work for their endgame paradise and not everyone is happy with that. I find some GregTech bits annoying as all hell(read: FUCKING SLOW MACHINES NOT PRODUCING MY SHIT FAST ENOUGH), but enjoy most of the mod without a hitch.
That being said, I have to find out how to set up one of the newer fusion reactors in GT(1.5.1 ones produce plasma cells which I then put in a plasma reactor, which seems OK but I know the layout for the coils changed), and after I do that, I'm going to make a spaceship and go to the moon.