Even though many Agilists can give a blank cheque in support of "open plan offices", we should be careful about implementing them without careful consideration. I have worked both in open plan and in cubicle offices. Each style has its own pros and cons.
My personal opinion is, seat arrangements should be "context dependent". One of the contexts I suggest to look at is the "type" of work. If the work involves more communication and interaction, then it is better to arrange that particular team in open space. However if the work involves solo, less communication/interaction work, then cubicle or closed room kind of design is recommended.
The office space could have separate designs within the same company while accommodating people with various work types. The R&D team ,specifically the researchers could be made to sit in cubicles to concentrate on individual researches. However the development team which need to communicate more often can be made to sit in an open space environment.
If the development team is made to sit in open space plan, then I strongly suggest applying "Caves and Commons" type. My personal experience is that, in the absence of "commons" people tend to receive and make phone calls all over the place distracting the people around them.
Even though I have been discussing about the infrastructure setup for Software development teams, it aids my belief that Agile methods should not be implemented in isolation trying to think only from the software process point of view, however the process should be applied by including various parties in a software company, like infrastructure, HR, finance, etc. The process should be applied end to end.
Local sub optimization won' t improve productivity !!
Another dimension to this discussion is, many a times we discuss about improving the "productivity" of the teams through various soft skills training, usage of expensive collaboration tools. However many companies over look the office space design. If the office space is dimly lit, crowded with ventilation issues, then no matter of what tools, techniques and process we use, it won't make much difference.