I've read a number of papers that compare the dozens of aligners out there. In general, they seem to agree that there is no "one best aligner" and that different software packages have different niches.
It seems like the general consensus is that bowtie2 and BWA-MEM are both great all-around tools.
When setting up your data processing pipeline, did you pick a good all-around aligner like bowtie2? Or did you experiment with other aligners before settling on something that works the best for your needs on your hardware?