If this Prestige Class didn't have "Learn Sphere Spell" (which is a pretty minimal benefit for a Wizard too) it wouldn't seem biased against Sorcerers. To ensure balance, I tried to avoid changing fundamental aspects of classes, such as the limited spell selection of spontaneous casters.
Note most players these days won't even think of taking a PrC that skips a casting level. (See Logic Ninja's #1 rule of prestige classing: "thou shalt not lose caster levels".) A Sorcerer might take your modified version, but then a Wizard would never take it. (Lose a casting level and 2 bonus feats, in exchange for 3 metamagic feats that can only be applied to sphere spells?)
Many PrC's, some with much greater abilities than Sphere Scholar, have full casting progression, such as
Archmage,
Loremaster, and
Thaumaturgist. I intentionally tried to make this a PrC with no casting level loss (which is why its abilities are fairly simple) and even then I was concerned people would think it's underpowered compared to others.