Bowtie2 is no longer the fastest aligner. Salmon and Kallisto are much faster, but have been designed to optimise RNASeq mapping. Their speed is gained from avoiding a strict base-to-base alignment. However, Kallisto can output mostly-aligned reads (i.e. position-only, without local alignment) as pseudo-alignments. See here for more details.
While Kallisto does bootstrapping that is interpreted by sleuth for improved performance in isoform detection, both Kallisto and Salmon can also output counts that are equivalent to read-level counts from other programs, which can then be used by other downstream gene-based differential expression analysis software (e.g. DESeq2).
HISAT2 is from the same group as Bowtie2, and does the same sort of stuff, but with a few optimisations added on top. In particular, it's much better at working out split reads from RNASeq runs. Like Bowtie2, it will do local alignment of reads.
For quick alignment of long reads, minimap2 works well. For high-accuracy alignment (but comparatively slower), LAST works well.
Most bioinformaticians seem to prefer STAR for things that Bowtie2 was previously used for. I'm not yet convinced it's a better alternative, and currently prefer HISAT2 for high accuracy short-read alignment.