Hm.
I don't enable aquifers. Too much work in my opinion. It really takes away from the game and creativity of embarks.
Psh, there are some hella-fun ways to pierce aquifers and non of them are really "hard." Double slit can be tedious but makes a nice neat stair-well. "Pump-stack" isn't as neat as double-slit, but a little quicker. It does rely on "dwarven hydro-reactors" so if you consider that an exploit its as no-no. That leaves cave-ins and freezing. Both of these are "messy" imho, because they leave large holes in the ground. Both rely on "concentric" squares (we can't really make circles in this game, now can we?) layers of stairs going down. Cave-in collapses floor after floor onto the aquifer, which destroys the aquifer tiles. you then have this giant pit with a staircase through in the middle. The freezing method will have a similar design in the end, but is only really safe to do in tundras or cold biomes where you have a long "winter." The point is to expose the aquifer tiles to the surface, which immediately freezes them. You can then dig through the ice. If you embarked on a cold (or temperate) biome, you'll have to channel out extra wide to place walls down for when the temperatures warm up. Either way, these last two methods (cave-in and freezing) require you to either know or guess the depth of the aquifer you are dealing with before hand. The problem is that you can never know exactly how deep an aquifer is beyond 1-layer without using cheats (DF-hack reveal).
Oh there are technically two more ways to pierce the aquifer. You can cast it in obsidian similar to the freezing method, but obviously this requires you to already have magma :p. The last is called "lucky as shit" because your aquifer didn't extent all the way through your embark, thus you can simply dig around it. You get all the benefits of an aquifer (infinite secured water for defenses/civilian use) as well as avoiding having to actually pierce it.
To me it ADDS to the challenge and creativity of your forts. You have to add in the aquifer to your fort design. This often means you can easily triple the amount of planned water-works for your fort! Drowning chambers are so easy to make! Even ones that fill/refill on their own. Your own reservoir is also so much easier to not only secure but set up. You can then start adding dwarven baths and even add "fountains" to your dining room.