Spread more of it around, but cut out premium bonuses so that no item is giving 20-25%.
Two items should NOT take you to the CDR cap. Just like there will be more life steal, but single items not giving as much, Most items with CDR should have 10-15% on them.

To compensate and allow for more itemization choices, actually increase the cap to 50%. This would also make CDR runes slightly better as you could push your total reduction higher.

From playing hide and seek vs. a Fiddlesticks I'd say CDR doesn't need to be any higher.

Also, CDR feeling underwheling is more a result of how it's represented as a statistic. If it were represented the same way as say, attack speed, 40% CDR equates to being able to cast abilities 66.67% faster. 50% CDR would allow you to cast abilities 100% more frequently though - each additional point of CDR you pick up is more powerful than the last, making it the only attribute that really scales exponentially with itself. I'm for more CDR options, but not for anything that would increase the cap beyond 40% reduced cooldown times.

There's a cap on CDR because it gets exponentially stronger with each point. I don't know the maths behind it and don't want to look it up because someone else will have it on hand anyway, but 50% CDR is much stronger than 40% CDR.