This is actually untrue for Geneforge 2 and 3. Creations gain experience (and therefore levels) at a rate totally indepedent of their own levels. Thus, if a Shaper creates a Fyora with enough bonuses to be at level 20, and an Agent creates a Fyora at level 10, the Shaper Fyora will always be 10 levels higher.
Also, Blessing Magic maxes out its effect strength (though not its duration) fairly quickly, so Shapers have no problem casting buffs that are just as good as Agents.