When he got the organics it had nothing to do with Wanda. It was this enemy called The Queen and she turned Spider-Man into a giant spider, as if THAT'S never happened before, and when he emerged from the cocoon of the spider he had organic webbing.
Though many writers haven't really stressed if he's still using his web shooters now or still using the organics. I've seen artists draw the web shooter nozzle on the Spidey suit after the organics so...maybe they're slowly sweeping under the rug.
But as far as any other upgrades and power increases...nothing comes to mind except the web shooter upgrades made during the Clone Saga by Ben Reilly. He made the web stingers and the impact webbing which really gave some kick ass new ways to stop the bad guys with his webbing.
Too bad Marvel didn't stick with this and had to sweep EVERYTHING from the clone saga under the rug like a bunch of cowards.