Well, age may be a consideration...
Goal Seek (I assume that you're talking about that which is found in the Spreadsheet function) is a much older function and while it's still fully supported and very effective, the Optimization function is much newer with a more modern interface and as as being better integrated.
For example, while Goal Seek is limited to using only Expressions, Optimization can also leverage KF objects as well as direct access to geometric aspects of the model. Also the 'solver' used in Optimization is based on modern and more powerful algorithms with more options available to the user for controlling how the solution is calculated.
Now they do both share the limitation the these are processes which the user has to launch himself (although I suspect that perhaps Optimization may have some NX Open support) and are not actually part of the model's behavior.
Now while we are talking about NX 6.0 here, I should point out that starting with NX 7.5 we have added an additional and more general tool using what some refer to as an Engineering Spreadsheet or 'Math Engine' supplied by a company named Maplesoft (the product name is Maple). In NX 7.5 we are providing an integrated interface to Maple (the interface is provided as an NX enhancement, but you will need to acquire the Maple software and license directly from Maplesoft). The big difference here is that when using Maple actual features are created which are imbedded into the NX model and which will update when the NX model updates (as long as you have Maple installed on the system when you do the update). Now I have not yet attempted to use Maple to perform something like an 'optimization' but it does have a very broad set of capabilities and anyone looking to do more complex problem solving and you're running NX 7.5, you give it serious consideration.
For more information about Maple and Maplesoft, go to:
John R. Baker, P.E.
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To an Engineer, the glass is twice as big as it needs to be.