Once of the design concepts behind the spells in HARP is that a caster can learn the basics of a spell/spell effect early on, and then it takes time and effort (i.e. DPs) to become fully proficient with the spell.
As others have pointed out, the way HARP is designed, you can either become very proficient in a few spells, or learn the basics in a larger number of spells.
As was also pointed, every PP invested into casting a spell above its base cost, gives a negative modifier to the spell, making it more and more likely that the spell will fail.
You mention darkness having a higher cost than invisibility. Yes, it does. But then again, Darkness affects an area, a radius, while invisibility affects a single person (no items) and has a number of conditions that will very easily cancel it before its duration expires (again, something that darkness does not have to contend with).
You mentioned moving to Hero... The spell creation rules for HARP were inspired by Hero. And guess what? Go create these two spells (Invisibility & Darkness) using the Hero rules, with all of the same limitations and aspects as these 2 spells have, and guess what you will see? Darkness will cost more than Invisibility.
Another spell that folks have issues with is the Light spell, saying that it is too expensive. Problem is, if it were repriced according the rules in CoM, it would come out MORE EXPENSIVE than it is now. The spells in the core rules were priced according to a prototype of the rules that were codified in CoM, and the core rules were subject to tweaking as well (usually to lower costs).
You mentioned increasing the costs of the spells. The question is why? And what is your reasoning for how much you wanted to increase the costs? The PP costs were derived from a set of creation rules, arbitrarily changing those costs would be unfair to your players, I think.
A much better solution is to just not make them available. Take a look at the professions in College of Magics. They are all Mages, but they do not all have the same spell lists for the their Sphere. In Cyradon, there are other Mage variants, and each one there does not have the same spells on their lists for their Spheres.
Do the same thing for your setting. Create magical orders, and have each order have a specific list of spells within their spheres and each variant does not have all the spells and each variant has different spells.
Or just create 1 order, but give it several levels of membership. Thus, beginning mages might have only 10-20 spells to select from. Once they hit 6th level, they are promoted to the next ring, and get an additional 5 spells added to those that they are allowed to learn, when they hit 15th level, they get promoted to the next rank within the order and get access to even more spells, etc...
What I am saying, is to not change the costs, but to change the availability and to work that availability into your setting through a logical reason.
If you think that mages shouldn't learn Long Door until 6th level, that is fine, then make sure it isn't available until 6th level, but don't just slap an additional PP cost on it just because you don't its current cost.
The spells in HARP are balanced, against one another and against the rest of the game. You might not like the way it is balanced in some cases, but that does not make its balance wrong. HARP was trying for some very specific goals and I think that it did well and met them.
However, that balance and those goals will not be identical for everybody. Nor will it be perfect for everybody. That was one of the reasons that we made HARP so flexible and easy to change without disrupting the overall balance.
