The Bam format was developed at a time when I/O (disk / network) was not a limiting factor for genomics data analysis. Currently it is. Especially when you have pipelines like GATK that process BAM files in multiple steps and read and write bam files for every step (instead of in memory streaming).

I know raw sequencing data (SOLiD & PacBio) and other large (scientific, financial etc.) datasets are stored in [HDF5](http://www.hdfgroup.org/HDF5/). And there are initiatives like [CRAM](http://www.ebi.ac.uk/ena/about/cram_toolkit) and [reduced bam](https://www.broadinstitute.org/gatk//events/2038/GATKwh0-BP-4-Compression.pdf).

Still I believe most organizations are using regular bam files. Why is this? Is there a roadmap towards development (and adoption!) of improved formats for storing DNA alignment data?
Neither of the solutions you have is a full alternative: HDF and CRAM are generic binary formats that could store any data. Neither is a specification (nor is it obvious that a SAM file transformed into HDF would actually be more performant than a BAM format). The reduced BAM format is not a generic format either, it is a simplified format that targets one specific use case.