It would be very interesting to have to assemble transmutation circles with regular materials and special blocks, according to certain geometric shapes. This way, extremely powerful transmutations would also require lots of work assembling a potentially huge circle.

Not only does this make the experience much more visceral than doing crafting recipe after crafting recipe, it allows for oh-so-evil transmutation requirements if you want to get some of the more powerful results. So you start raising loads of sheep only to build a gigantic transmutation circle right on top of and around the pasture. Or worse, the poor villagers wonder why you're tracing these weird geometric shapes around the village. In some cases attracting the proper creature(s) into the circle would be a real challenge, if you need an enderman or a ghast for instance.

Great idea! what i thought was to have 1 transmutation altar that would be made in-world like with obsidian or stuff and then you have to learn circles like "Lvl. 1 Fuel Transmutation Circle" and combine different Circles to Transmute different stuff like: glowstone is Matter but it is also considered as Fuel and can be only obtained going through the Nether....
so you need to combine a "Lvl. 2 Fuel Transmutation Circle", a "Lvl. 1 Matter transmutation Circle" and a "Nether Transmutation Circle" to get an altar that is able to transmute glowstone for you to learn it throw one in the circle and a lightning strikes (just for awesomeness) and let's assume it has like a 1000 emc value you'll have to throw 1000 dirt in the circle to get one. and just for the record, every circle has its own rendering like if nether transmutation circle is a pentagram (a star in a circle) and if tha matter transmutation circle is a pentagon when you combine these two it'll render as a star in a pentagon that's in a circle. and it'll be like a "Nether Matter Transmutation Circle" a lvl 2 matter transmutation circle would be a pentagon within a pentagon (yeah so nice!) s

A few more things to complete my idea above:

I think that for my idea to work you'd need visible in-world templates (like glowing transparent blocks) to show you where to place stuff. Or anything that prevents you from having to keep a wiki open at all times, really ;) .

In the OP I mentioned animals and mobs, but you could also transmute a forest or your crops, besides of course inanimate matter.

For really powerful items like the philosophal stone, the transmutation circle should probably be one-use.

Sounds a lot like a mod I started making a while ago, before I found out about EE. Since EE was already finished and the ideas were so similar I decided to scrap what I had, but if EE3 doesn't incorporate this and has an API that's easy to work with, I might make an add on that does this. It'd be kinda nostalgic.