Mmm, first of all:
Diamonds. Yeah, true, you CAN get diamonds from cobble.. but it takes some time and energy usage.. EE3 is not free. It just makes things easy, of course, you could limit yourself. Thats what I do. For example, i do not use industrial diamonds for vanilla (or other than IC2) stuff, i don't care if they're the same in the forge ore dictionary, i just don't use it. And, if we are talking about diamonds.. EE3 isn't the most OP situation.. have you ever tried mystcraft? In my current world, i got a dense ores page.. And im gratefull that i have EE3, because i can turn diamonds into iron (Yes.. Diamonds into gold, then iron..). Mystcraft dense ores is the most OP thing i've seen. 15 mins with a diamond drill is worth from 1 to 2 stacks of diamonds. I just don't even take them anymore, i use mystcraft dense ores to get coal and iron, sometimes redstone but because of my fortune enchantment, i can mine for those in the overworld pretty easy.
The thing about EE3 op'ness is right, maybe you can get a diamond pick in the first 20 min of gameplay if you play your cards well and find iron.. Yeah, im not going to discuss that.. But that is your decision to make.
Second: EE3 is so fucking usefull. I use it for this, the most of the time:
Turn cobble into dirt. I tend to construct with cobble (in a filler) and i like alive roofs.. So i turn the roof into dirt. Easy. No breaking blocks.. etc..
Turn Wool into its colored counterparts.. I don't like to mix things to make colors.. I limit myself and i do not change to the basic colors like white, black and red / yellow / blue, because they have fair obtainable dyes without too much crafting shit.. Another thing i find cool but i prefer not to do (i did it, but only once, because i didn't found a desert biome.. it was like 700 blocks away :S) is to change dyes into green dye to make waterproof. i usually use waterproof only in start game, then i just go to liquiducts.. but its cool.. and somepeople may find it awesome (more if using Extrabiomes.. which, yeah, adds a lot of biomes, but while doing that, it's less posible for a desert biome to spawn)
Third:
Variety.. Yeah, as stupid as it may seem.. I HATE basic constructs.. I like to use different kinds of rocks and wood (achievable only if you get the saplings.. and EE3 helps with that) in my cosmetic constructs.. Of course, you could transmute and get Jungle, yeah, may be a little op, because the wood of a jungle tree is 4 to 5 times more.. Again, i limit myself, and you could do so too. And for the diamonds part of wood.. yeah, you can get diamonds from wood.. so what? You know how much wood it takes to make a diamond? A LOT. you're better finding them in the caves.
I think it would be cool to have a little.. mm.. unequivalent exchange.. for example, needing more gold to get a diamond, and getting less gold from a diamond.. like if some of its "value" is lost in the transmutation.. I would really love that..
For the minium stone being cheap, yeah, i think it is, so i made it less durable, go to your configs folder and you will find a durability conf for the minium and pilosoph stone, just tweak it according to your plans. Mine can endure just one transmutation. Just put 1 in the durability. Another cool change is the durability use of items or blocks, tweak it and you can easily config whats easier to trade. I tweaked it so i could not get more than 1 block transmut and more than 2 item transmut per stone.
Its just a matter of what you like or not to do. I decide not to use some of it functions because i feel they're not fun at all.. And i decide that some of its functions are really usefull and not balance breaker.
Again, if you want diamonds go to a mystcraft dense ores age.. you need to get the page.. but you can just use an automatic farm to get wheat and sell it to villagers.. then, exchange emeralds only on the myst vilaggers and you're done, in no time you will have dense ores.. (which is worth 45 emeralds, i found it twice, and i buy it and drop it, so i could get to the next page...) EVERY SYSTEM IS OP IF YOU KNOW HOW TO USE IT.
I just try to use the most difficult option for everything, i just go for easier ways when i feel there is no fun in the hard way (i HATE long crafting recipes, or checking nei all the time, so, for example, dyes..), even more if its just a cosmetic change like transmuting an oak sapling into birch to get white wood.
Im just waiting for a config file to modify my transmuting recipes ( by now, i limit them myself.. for example, trading wood for obsidian, for me, it takes 9 wood, i just do the mats and drop the wood into a void pipe. Simple, and i feel its still, fair. 9 wood for 1 obsidian? Ill take it, my cart with diamond wood cuttter saws will take care of the rest.)
