Research is not finished on this topic, as one can see from recent papers.
Newer studies than those cited not only confirm the statement on gut flora but go further, namely that other habitats, not only the gut, are impacted:
We found that in direct contrast to the highly differentiated
communities of their mothers, neonates harbored bacterial communities
that were undifferentiated across multiple body habitats, regardless
of delivery mode. Our results also show that vaginally delivered
infants acquired bacterial communities resembling their own mother's
vaginal microbiota, dominated by Lactobacillus, Prevotella, or
Sneathia spp., and C-section infants harbored bacterial communities
similar to those found on the skin surface, dominated by
Staphylococcus, Corynebacterium, and Propionibacterium spp.
Dominguez-Bello MG, Costello EK, Contreras M, et al.: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. In: Proc. Natl. Acad. Sci. U.S.A.. 107, Nr. 26, Juni 2010, S. 11971–5. doi:10.1073/pnas.1002601107. PMID 20566857. Free full text
A recent review concluded
Given the complexity of the gut micriobiota, additional research is
needed before we can confidently establish whether its manipulation in
early life can prevent or treat asthma, obesity, or both.
N. P. Ly, A. Litonjua, D. R. Gold, J. C. Celedón: ''Gut microbiota, probiotics, and vitamin D: interrelated exposures influencing allergy, asthma, and obesity?'' In: ''The Journal of allergy and clinical immunology.'' Band 127, Nummer 5, Mai 2011, S. 1087–1094. doi:10.1016/j.jaci.2011.02.015. PMID 21419479. Free full text
So, please ask this again in three or five years. However, the fact that gut and other flora are greatly influenced by delivery appears to be without question, and is in itself an argument against Caesarean, IMHO.