OP already stated that the arcane thesis spell is scorching ray, so his area spells are just using his native caster level. That said, forcing him to change his race and feats arbitrarily is a terrible idea.

Not only is whisper gnome not a particularly optimal choice for a wizard as compared to many other options, but arcane thesis is neither broken in general on its own, but is not overwhelming in particular when applied to scorching ray. At level 8 with the +2 CL boost he's not even gaining a damage boost from it currently due to the way scorching ray scales. On top of that, the individual rays give it a much greater level of vulnerability to fire resistance of any kind, and it's SR:Yes.

While he has certainly taken some good options, nothing he is using is really optimized. He just picked a pretty good race and a good feat. Don't penalize him for that.