Before I get started, let me clarify that I have no issue with the three level rule for each class. I approve of it because it effectively prevents a fair number of cheesy power builds. My issue is with the requirement that you have three levels in each class prior to level 20. This rule doesn't effectively prevent power building and can even get in the way of other builds.
I'll admit, this discussion came about because my build violates it.
When I first designed it (two?) years ago, I knew about the 3 rule but had forgotten about the 20 rule. By the time I realized the future problem, I was already well past 10. I had hoped it would be okay because the third level in my last PrC would be taken right on 21 without providing any "epic" benefits.
I actually wanted more than 3 levels in the PrC before 20. It would've made my character much stronger earlier. The combination of PrCs require exactly 7 feats and my character is a non-human/halfling. I wasn't able to take the first level in that PrC until level 19 because the last non-epic feat can't be taken until 18. As you might now realize, attempting to reorder the PrCs won't make a difference. (I spent a long time trying.) I'll have to abandon my build even with an RCR.
It's not a power build either. (Or not what I would consider one at least.) The "main" PrC it was built around is the Bladesinger. So my base is an elf wizard, right? Wrong. She's an elf sorcerer. If my character were a wizard, not only would I avoid the feat issue (wizard bonus feats), the character would be a lot stronger because of the INT bonuses. I could even focus on Int & Dex, take Finesse (Rapier) & Combat Insight, and be a melee powerhouse with epic spell casting by level 23.
She's a sorceress. Though there were other options that would have synergized better with her high charisma, the Bladesigner and other PrCs I've chosen better reflect her story.
The rule can prevent non-power builds, and I'm sure others have run into similar problems with it in character creation. So I think it'd be good to discuss the rule, see if it has a valid purpose, and/or find a better way to fulfill its original purpose: limiting power building.
For example, the first build that comes to mind that the level 20 rule seems designed to prevent is the fully epic Divine Champion. The PrC can normally get an extra 5 epic feats if you start the class at 21 (or 20). The level 20 rule makes it so only 7 levels of DC can be epic, reducing the bonus epic feats to 4. That being the case, wouldn't it be better to re-balance the class itself?
Base classes are also affected by the level 20 rule. I'd be willing to bet that the Monk class was largely considered with the numerous power builds that take a single level just to get the Wis AC bonus. Bard/Sorcerer RDDs as well with the reintroduction of the RDD. Of course, the 3 level part takes care of this, but without the 20 rule, it'd be possible to be a level 1 monk/ninja or sorcerer/bard until level 28. It's times like these I agree with the level 20 rule, but I think it would be better if it was limited to these specific situations rather than a blanket rule on all builds.