In regards to spells countering monster's nasty effects; one way is to use the same spell to counter it. Just like the existing system. I just state I reverse the effect with the same power. Another way is to create a building block for 'restore', for 'release' or for 'replenish' and coupled with other building blocks have the ability to remove negative effects.
This could potentially work if the Restore/Release/Replenish portion of a spell can be added on
for free. If it is not (and requires you to gain another level, or whatever, before it can be used), you are going to have a situation where monsters of level X can hit the party with effect Y, and the party cannot counter/deal with effect Y until a level
later than X.
And making it "free" could be workable. If each player has a certain number of "known effects" that it can stack, and can only stack so much based on their level, the "clerics" would blow one of their known effects on countering, which would be a cost to them, even if they can stack "Remove" on top of "Blind" to get Remove Blindness, and have both of those be the same effective level.
The one side effect I see with this solution (I won't strictly call it a down side) is that then, in order for you to be able to counter X, you have to be able to
do X. So, in order to remove blindness, diseases, and petrification, you need to be able to blind, cause disease, and petrify. In order to be able to counter fire damage, you have to be able to
deal fire damage. Not necessarily a problem, but it might make your characters look different than you were imagining.
Actually, it's the exact opposite that happens.
If the PCs have gate/wish/genesis/planar binding and whatnot, the campaign story will always start and end with "and our infinite army of solars/titans/prismatic dragons took care of every problem while we were sitting in our super safe plane where nothing can hurt us and we have negative reasons to leave". There's really no story-telling at all. Nothing in any MM can hope to challenge the party, in particular because the party can just spam the best monsters do to their bidding.
If you want to tell a story with D&D 3.X, the first rule is to nerf/remove the hell out of at least half the spells Strat mentioned. The game completely breaks if you use gate/wish/genesis/planar binding and whatnot as they are.
We're getting somewhat off topic, but yes, a lot of effects need to be fixed to work. Removing them is one way to do that, and addressing the problems is another. The first option yields "low level" games, and the second would yield "high level" games that (supposedly) work better than they do, now. I consider this a separate issue from whether or not spells should be made up of stackable low-level effects.