It's kind of self-defeating to have a leveling system that is a convoluted point-system requiring cash items/very annoying quests to reallocate every once in a while for maintenance...
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It's indeed very hard to understand for people who didn't play the game in open beta, or early launch; allow me to explain the history of this.
Originally, you could max all 15 spells; the idea was that your character level didn't really mean anything, and your progression in the game was supposed to be determined by the spell levels themselves (sounds like Skyrim in a way, doesn't it?). There were a few problems with this system however; first of all, the gameplay meta when the game launched, was essentially that you spammed one spell repeatedly, until you reached level cap (100 at the time), and then maxing another spell was very time consuming (some have said it was the same as levelling another character from scratch, but it wasn't quite that bad; it was still very bad though). This problem was compounded by the fact that spell exp gained in battle is divided between all spells used in battle, and in a huge oversight, Ankama made it so that even a maxed (lvl 100) spell, would STILL cause exp to be divided, which meant that you couldn't just use the spell you want to level, and then cast your lvl 100 spell to actually do damage on the next turn; you had to basically just use that low level spell until it was actually capable of doing any damage, which obviously works best if you're being powerlevelled, that way you could cast the spell you want to level, and let someone else do the actual killing.
So, why did they change it? Well, as you can imagine from what I've said above, very few people actually bothered to level all of their alt branch spells because it was the most ridiculous timesink imaginable. There were a handful of people that did it though, and back then, spell levels gave you resist in the element in question, not just damage like now (resist was also absolute back then, which meant you could actually reduce damage taken to like 1 final dmg per hit, rather than only reducing down to base damage), which essentially meant that there were a handful of extremely overpowered individuals running around, who were relatively immune to damage in three elements, and had ridiculous damage from having all spells maxed in their main elemental branch. As you can imagine that was a pretty nasty combination in PvP, higher damage than any other player on average, and higher resist than any other player on average; many people complained and the first "spell revamp" was Ankama's eventual response to these complaints. Originally we could only have 2 maxed spells at level 100 in one elemental branch, and we were supposed to get 4 when lvl 200 would come around (spells only went up to 100 back then, even while the cap was 110 and so on), but then they changed it to be linear like now, where we can have 4 spells for mono element, 5 for hybrid, and 6 for tribrid.
Anyways, that's the history lesson out of the way. So as you can see, the game has changed quite a lot, and the current spell system is really a relic of the past; it basically is the way it is due to it's evolution over time, and I imagine the next spell revamp is aimed precisely at changing this to make it feel more consistent. They originally wanted the game to be different from Dofus (where you apparently stat your spells as if they were specialties, I think), but in the end, Wakfu's spell system pretty much evolved in the same direction; the spell exp system now is more or less just another point-statting system, where the spell exp is your "points" and you just stat them into spells. Personally I'm hoping they get rid of the hybrid/tribrid spell exp bonus and just allow all of us to get like 6 spells or something (I'd love to have 7 or 8 though, to be honest, since I'd like to get 3 spells in two different branches, and then one spell in third branch or something like that).
I hope my wall of text wasn't too annoying to read, and I hope I've shed some light on the spell system's history and the reasoning (or lack thereof) behind it's design. =)