I consider the problem you've explained as a necessary evil. Without items, spells, etc. following a structured format, the system at large runs the risk of becoming unbalanced. With classes like Wizards, Clerics, and other full casters, the system requires a lot of magic items to allow the other classes to keep up. The system EXPECTS you to use them to keep up with the MONSTERS of the same level. Those magic items need to be created very carefully, thoroughly considering the rules and limits of each, or else you suddenly have the other classes even more powerful than the full casters, or else you've allowed full casters to widen the gap even more. Worst-case scenario, you've made all the classes too powerful, and they defeat the monsters too easily and the game becomes un-fun. If magic items are ambiguous, you're inviting them to be exploited. Yes, a better system would have made all classes equal on their own, but we'd need to completely rebuild all the rules in order to pull that off at this point.
No matter how wonderful and unpredictable a game's design is, its players will eventually become disenchanted after playing it enough. Pathfinder has made it this far because Paizo has been successful at introducing new mechanics, classes and even genres for its customers to play, keeping the otherwise unchanged game feel fresh. Obviously, they're not going to keep ahead of the curve for everyone, and not everyone is going to love each new book.
In my opinion, this problem hinges on the GM more than anything else. The GM has the power to alter the game in ways that no rulebook could ever do, and do it according to his players' preferences and playstyles. He can make the game feel more grounded by banning full caster classes, or removing casting classes altogether, giving magic that spark of mystery and wonder that you mentioned. He can use a spell or magic items listed effects and make them manifest in narratively different, yet mechanically similar ways, so even players who know the game's spells and rules front-to-back are suddenly seeing something new.
So, if you feel like the game has lost its feeling of wonder, I suggest talking to your GM about changing things up. Maybe try something totally different - maybe have everyone play a class from Occult Adventures and play a game using rules from Horror Adventures and Ultimate Intrigue. Now you're playing a creepy game of mind-tricks and social subterfuge - miles from the traditional dungeon-crawling system Pathifnder was originally built on.
Did you ever play AD&D? Magic items were quite a bit more rare in it, and much more difficult to craft. Some monsters were also literally immune to damage from a weapon with less than a specific + amount. Having magic items be less common didn't add wonder so much as it meant you had to use whatever dropped/turned up in the loot pile or you could end up completely out of luck.
Pathfinder isn't quite that bad, but ask a two weapon fighting type who has fought a creature that has 5 or 10 DR how much wonder they'd feel without reliable access to magic weapons to fight it. :P
Have you considered automatic bonus progression? This optional system replaces a lot of the items needed to keep up with increasingly powerful monsters, letting the players focus on magic items that might interest them more.
As far as magic goes, while the mechanics are set the fluff can usually be changed with little fear of unbalancing the game. For one character magic missile fires white glowing arrows, for another red flaming skulls ect ...
Magic items can also be given more detail than just "this is a +1 sword", which may increase their appeal and wonder, to a degree.
Many spell casting classes have the option to research spells, you'd need to work with the GM on the specifics of the spell in question.
In Pathfinder specialization is usually encouraged, meaning if a magic item isn't in line with your characters purpose, it's usually considered not worth keeping. This could be as simple as a character who focuses on a specific weapon (or type of weapon), or a caster a certain types of spells (buffs, damage, save or suck) each has a different approach to maximizing their effectiveness.
With many GMs I've played with magic item selling and buying wasn't always a guaranteed process. The potential seller may not have exactly want you want in stock, it's often dependent on the GM. I've also had Gms who have tried to scam the PCs in various ways when they tried to sell magic items, but I wouldn't say I really enjoyed it personally.