Both systems will help address acne, but they are different systems. With the Nu-Derm system you get the added benefits of hyperpigmentation reduction and anti-aging effects. Clenziderm will mainly just treat acne. The Clenziderm system does not contain hydroquinone products.
Background info about CLENZIderm from OBAGI
Obagi CLENZIderm is a prescription strength acne treatment that has a patented, solubilized 5% benzyol peroxide which penetrates deep in to the follicle to treat acne at its origin. There's a Oily and Dry skin version of this product (just as with Nu-derm). The manufacturer says that their benzyol peroxide has better penetration therapeutics than others because of CLENZIderm's much smaller size.
Background info about Benzoyl Peroxide
Works by killing bacteria and reducing inflammation in the follicle
Higher strengths doesn't necessary improve therapeutic benefit. Better penetration may be the key (as in the Clenziderm system)
Use once or twice per day
May cause skin irritation
May bleach hair or fabrics (ie. your pillow)
Shouldn't be used at the same time with Retin-A / tretinoin because benzoyl peroxide inactivates it.
Regarding Cost of OBAGI Nu-derm and Clenziderm
If you are out of a few products in the Nu-derm system, you can buy the products individually to replenish your system. This might cost less than buying the whole Clenziderm set - which is a new system.
The pricing (as of this posting) of a Nu-derm starter set costs about $394, and the pricing of a Clenziderm Starter Set is $130. Tretinoin costs $73-83 depending on the strength.
To continue on the thought from one of the paragraphs above on replacing a Nu-derm product: One of the most important products in the Nu-Derm system that is frequently used up/replaced is the Nu-Derm Clear which costs $91 for a new replacement bottle.
Combo possibility
It is also possible that for certain patients, one can combine these two systems for desired effects (using mainly Clenziderm in the morning and nu-derm at night -- not at the same time due to degradation of Tretinoin). Please see your doctor in person to see what is best for you.