I think I just disagreed with it 
So random exmple:
Fireball does 10 damge. One shot per second. -> 10 DPS
Now you have two upgrades: More damage and more speed.
Now let’s assume, for balancing reasons, an upgraded fireball should do 100 DPS.
If you allow both skills to be upgraded, and want to get at 100 DPS
The more damage upgrade allows you to raise damage to 50.
The more speed upgrade allows you to raise speed to 200%.
-> That’s 100 DPS.
If you make those two upgrades exclude each other:
The more damage upgrade allows you to raise damage to 100 (twice as high!)
The more speed upgrade allows you to raise speed to 1000% (five times as high!)
Both of those create 100 DPS on their own.
I did not reply to your example last time as I thought it is just a bad example, but this time I will as you keep bringing it up.
In this case you created two skills which accomplish the exactly same effect in two ways, making one skill completely redundant. If this is your idea of having to make an ‘exclusive decision’, then there should not be exclusive skills simply because of that. Anyone not going with the faster speed doesn’t understand game concepts, it will always be the better choice.
I do not want skills which achieve the exact same thing in two ways (even if neither were clearly superior) and then call this mutually exclusive. Just roll them into one and do not even have the other. If they are to be exclusive, they at least should accomplish different things, not the same thing.
A better example imo would have been a fireball with identical damage in an increased area versus more damage in the same area.
So in order to allow all enhancements simultaneously, you have to limit their power. Then you are limited too. Your spell can neither get as fast, nor have as high damage than with my idea.
I got that, I did disagree. In that case, do not create overpowered skills, as I said before, they already are exclusive as I can invest a point exactly once. No need to actually make skills which are mutually exclusive, this does not offer more diversity, it offers less.
As a refinement to my proposal:
That two enhancements do not need to be strictly excluding each other, so that you can only either raise the one OR the other. It’s just important that both in combination, stay within the maximum allowed power of the spell.
So maybe, if both enhancements could have 10 ranks - then say the limit is 10 ranks for both of them combined.
So you could level both enhancement skills to 5-5. Or you could do 10-0 or 0-10… or anything inbetween.
You claim this to be a limitation - but I really don’t think it is.
I certainly would prefer this over enforced exclusive skills. I still do not like your example as the result is the same, so it makes little difference what exclusive skill you choose. In that case, just offer one. The effects should be different, not the same. If they are the same it is not an exclusive skill, it is a redundant skill. But that is more a flaw in your example than in the approach.
You can simply view this (limiting the number of skill points invested in a tree to a number lower than the maximum) as an argument against overpowered skills however. But I certainly like it better than making skills mutually exclusive.
I still am not sure why I should not be allowed to take both, as this means I will not be able to take a third skill, say increased fire damage for all skills, which would also help me.