there are several factors to be optimized

1. Machine Flexibility

2. Routing Flexibility

3. System Flexibility

In case you are designing supply chain you need to look at supply chain flexibility.

I suggest that you look into the following literature 

1. The fundamental principles of flexibility in manufacturing systems

JA Buzacott - … of the 1st international conference on …, 1982 - North Holland Publishing Co.

2. A generic approach to measuring the machine flexibility of manufacturing systems, EJOR 

3. On measures of flexibility in manufacturing systems

P. H. BRILL & M. MANDELBAUM

Pages 747-756 | Received 01 Nov 1987, Published online: 28 Mar 2007

IJPR

M.I.M. Wahaba, , , Desheng Wub, Chi-Guhn Leeb

There are several other authors, but suggest Buzzacott and Brill et al.

I hope it helps.

Regards,

Goutam Dutta

If I were in your shoes, I would start by asking myself what would I find worthwhile to optimize (aka, defining the objective function and the variables) and to which extent this particular optimization would have an impact in the real world.

In addition to the reads that Goutam suggested, I recommend taking a look at these two articles (see links):

the first one comes up with a summary of the different "levels" of flexibility in a FMS and how they link to each other (I refer to page 297)

the second one is a particular type of optimization that involves environmental aspects as well, considering production costs and energy consumption costs. 

Best

Ilaria

https://link.springer.com/article/10.1007/BF00186471

https://link.springer.com/chapter/10.1007/978-3-642-29069-5_70