Well Plate Method VS Kirby Bauer Method
I came across a nice Master's thesis that investigated precisely that. The conclusion reads as follows:


  Automated microbroth dilution-based testing methods are increasingly used by many
  clinical microbiology laboratories to determinate antimicrobial susceptibility. Thus, it is vital that
  these methods are able to accurately determine the correct antibiotic susceptibility patterns of
  microorganisms being tested. In our laboratory, we use the Trek Sensititre system (Well Plate Method). However, if
  this system cannot accurately detect resistance visualized as inner colonies on the Kirby Bauer
  Assay, then the clinical importance of the Trek Sensititre may be called into question.
  
  Our study showed that the Trek Sensititre was unable to detect the
  additional resistance of inner colonies that are detected using the
  Kirby Bauer Assay. Nevertheless, there are a number of important
  limitations associated with the study: Firstly, the inner colonies
  used in the study were pooled from all inner colonies from the Kirby
  Bauer plate. Because the colonies were pooled, in some cases from
  different antibiotic zones, it is possible that a mixed population of
  resistant organisms that were selected for by the different
  antibiotics were tested. This possible mixture of multiple different
  subpopulations may make the results difficult to interpret. Secondly,
  some inner colonies were selected from antibiotics that do not have
  any CLSI- 47 approved interpretations and would be considered
  inappropriate to report. For example, some Pseudomonas aeruginosa
  isolates displayed inner colonies to ertapenem, an antibiotic that has
  no CLSI interpretations and a drug that would not be used clinically.
  The Trek Sensititre results from those inner colonies showed
  additional issues with multiple different antibiotics. Clinically, the
  patient would not have been treated with that antibiotic, so that this
  resistant set of subpopulations may not have been selected for. Thus
  the results from the study may not be clinically significant but it
  does open up questions to the possibility that the Trek Sensititre may
  not detect clinically significant resistant subpopulations. 
  
  Given that
  the Trek Sensititre can miss resistant subpopulations in Gram negative
  bacilli, it is important to establish the clinical relevance of this
  finding. If the inner colonies selected for by each of the antibiotic
  discs was sub-cultured individually instead of pooled together and
  then run on the Trek Sensititre, then the following results may
  possibly differ from the pooled inner colonies. An important future
  direction would be to determine whether the unreported resistance from
  the organisms in the study had an effect on patient care however, this
  was beyond the scope of this thesis study. Thus, the clinical
  significance of this study’s findings require future study.
  Nevertheless, laboratories should be aware of the potential for
  missing sub-populations of antimicrobial resistant organisms using
  broth-based microdilution methods.