While I use Bowtie2, there is not a strong argument for it versus other genome aligners. I guess it is because I found a pipeline back in the day based on Bowtie2 that did the job, and had no reason to switch.

You probably don't need splice-aware aligners, which gives you more options. The following paper might help:

https://academic.oup.com/bioinformatics/article/28/24/3169/245777

Even though some more recent aligners are missing in that paper (minimap2, salmon and kallisto come to mind), it should give you a good idea about available options.

+1 for bowtie2. Also because it just does the job. If large indexes become a memory problem or if you do not want to use a local-aligner but a global-aligner, consider BBMAP.