Currently when calling variants you have to call variants on all people simultaneously, which allows for rare variant positions being check and called in every person without such variant.

My question is, why wouldn't it make more sense to just determine variant in every genomic position (3.2Billion) and that's it? You could merge this dataset with others easily, moreover, no need to do joint variant calling etc. It is very frustrating to see such an inefficiency becoming default.
You are correct, but you have conflated two issues - variant calling and warehousing. First, I don't think you will see joint genotyping being routinely done in 5 years - single sample calling with instrument-specific training sets are where things are headed. Secondly, the bigger groups are moving or have already moved to variant warehousing rather than VCFs - TileDB, Google Variant Transforms, GenomicsDB - and these want gVCFs as input.