So, I set out to balance all of the effects accordingly. The positive effects have remained as true as humanly possible to the original settings, given that I've removed a few positive effects to curb abuse issues (fortify intelligence, fortify luck, and fortify fatigue) and added a few new ones (jump, shield, slowfall). All of the negative effects, on the other hand, have been balanced to be more appropriate to the positive effects they are trying to counter, as well as making them show up in potions more often than before, generally requiring higher quality ingredients to brew downside-free potions. Drain magicka, drain endurance, and drain personality have all been removed as negative effects, since they weren't very negative.
Amazingly, I managed to stay (hopefully) pretty faithful to the game's original settings. While nearly every ingredient in the game has been edited in some way, most of the edits are either to the negative effects (which most people probably don't pay attention to, anyways, since most of them would never actually show up) or to the positioning of the effects. The readme file in my mod when I finally finish the update will go into a bit more detail, but I just wanted to get some more immediate feedback while I was still working on it.
I suppose I could just post a list of the ingredients I've edited, but it seems like the changes I've made would probably be much more apparent if I listed all of the ingredients by effect. Incidentally, I created a file doing just that, which I am considering including with my mod as sort of an "extra" for people who want a quick reference to the new effect settings. Yes, no, maybe?
Here are the new effects (EDIT: I've whipped up[ something hopefully a little easier to read, that I intend to include with my mod):
http://btb2.free.fr/temp/alchemy.html
(My main concern, FYI, is that I've inadvertently made any one effect way too difficult to achieve without seriously adverse side effects.)
http://btb2.free.fr/temp/alchemy_changes.txt
And that's the full changelog, so you can see the context of the changes, along with the changes to pricing, weights, and the pre-made potions.