My end goal for the game is usually complete and total automation of everything, no matter what I have to go through to do so. Last time I was playing this pack, i was working on the automation of the Thaumcraft infusion altar, which seems impossible but it really is not, given OpenPeripherals is installed. A bit of coding (ok, a ton of coding), and it is possible, and the ME system makes it easier if you have a sub-system dedicated to just thaumcraft.
As for Mekanism's fusion reactor, i use it because it puts out anywhere from 200,000rf to 9,800,000rf per tick, depending on the injection rate. I usually run mine at an injection rate of 10, so 1mil rf/t, because its handy to have when you have multiple quarries running, a tier 5 ore processing plant, a huge ME system, including quantum rings and wireless connectors, etc. I then route all of my power from the reactor to a 7x7x7 induction cube (from Mekanism) with the elite everything inside it; so about 25 elite providers and 100 coils, so it can hold about 20,480,000,000,000 rf total. I checkerboard the outside casing with ports so that I can put Dimensional Transceivers all over it, to provide power to whoever or whatever I need (if you do this, make sure you use a configurator to shift-right click each port to set them to output mode). I connect this matrix to the reactor with a Cryostabilized Fluxduct, so that there isnt any loss. The only issue with this reactor (considering that it will NEVER explode) is that the 9 thermal evaporation plants, 8 rotary condensentrators, 64 fully speed upgraded resonant aqueous accumulators, and 20 solar neutron activators cause MASSIVE lag, so you have to quarantine them about 4000 blocks away from your base in a desert. Otherwise you lose efficiency and you get a lag attack, which is horrible. I usually dub the area "lag desert" because not only is it super laggy and a desert, it has to be chunk loaded so that you constantly create fuel for your reactor. If youd like to try to make one some time, a really great guide can be found
here.
For quarries I usually go with about 4-8 ender quarries, each mining a 1000x1000 block area, with 3 speed upgrades and a pump upgrade. They get their power from, and send all items through, a Dimensional Transceiver, which then sends the fluids and blocks into the ME system directly. The easiest and quickest way to do this is to use Interfaces (one fluid, one normal) attached to the DT, because the DT wants to put things into an inventory, and the interfaces count as one. Just make sure the DT is set to push items/fluids into the proper interfaces!
Once I get my main base up and running (ill attach a picture of the birds-eye view and maybe one from flying), I start with Thaumcraft, grind for a few days until that is complete, then I start work on Botania (i love this mod too, its so much fun!), and then finally I work through the quest tablet, and get everything completed. I usually, after getting the fusion reactor online, use the surplus energy to get a ton of coins via the RF submission block, and the Bulk orders tab in the quest tablet, so that I can turn them into Green Heart Canisters for me and my friends. Keep in mind (because i did not know this) that if you put an exchange token in your crafting grid, one token makes 64 more tokens!