set.seed(1)

df1 <- data.frame(id = sample(LETTERS,50,replace=T), val = rnorm(50), val1 = rnorm(50), stringsAsFactors = F)
df2 <- data.frame(id = sample(LETTERS,30,replace=T), val = rnorm(30), val2 = rnorm(30), stringsAsFactors = F)

df.list <- list(df1,df2)

library(dplyr)
df <- df.list %>% purrr::reduce(dplyr::inner_join,by="id")

id       val.x       val1     val.y       val2
1  G -0.05612874  0.2914462  2.087167  0.7876396
2  G -0.05612874  0.2914462 -0.255027  1.4411577
3  J -0.15579551 -0.4432919 -1.286301  1.0273924

df.list.colnames <- unlist(lapply(df.list,function(l) colnames(l %>% dplyr::select(-id))))
df.list.colnames <- table(df.list.colnames)
repeating.colnames <- names(df.list.colnames)[which(df.list.colnames > 1)]

repeating.colnames.df <- do.call(rbind,lapply(df.list,function(r) r %>% dplyr::select_(.dots = c("id",repeating.colnames)))) %>%
  unique()

for(r in 1:length(df.list)) df.list[[r]] <- df.list[[r]] %>% dplyr::select_(.dots = paste0("-",repeating.colnames))
df <- df.list %>% purrr::reduce(dplyr::inner_join,by="id")