Why Illumina if PacBio provides longer and better reads?
There are so many reasons why one might want to prefer Illumina over PacBio (also note that it's a false dichotomy, at least Oxford Nanopore is a competitive sequencing platform):


The first (IMHO and the most common reason) is still the cost of both sequencing and the instruments. Illumina can sequence a Gbp of data for \$7 - \$93. PacBio sequencing is according the same webpage \$115 per Gbp, however at our sequencing center it's ~$200. Though ONT might have already a cheaper solution. Edit, I just found a google sheat with prices that seems to be frequently updated, seems that the ratio still holds Illumina short reads ~10x cheaper than PacBio.
RNA-seq (i.e. analysis of a gene expression) is not possible with PacBio due to preferential sequencing of smaller fragments; shorter genes would always be shown to be more expressed. To be clear, it's possible to sequence RNA with PacBio (the keyword is iso-seq), but the analysis of gene expression is problematic.
It's way easier to extract fragmented DNA (concerns small non-model organisms; although recently a single mosquito was sequenced, so we can expect a further improvement)
other sequencing techniques as RAD-seq that allow genotyping with very little effort and cost, I have never seen anybody even considering using long reads for such genotyping
Genome profiling (assembly-less genome evaluation) based on kmer spectra analysis is not possible with PacBio data due to higher error rates. Conflict of interest: I am a developer of one of the tools for genome profiling (smudgeplot)
DNA in Formalin-Fixed Paraffin-Embedded samples is fragmented anyway (~300bp), therefore, there is no point in sequencing them with more expensive long-read technology (contributed by @mRoten)
I bet there will be a plenty other applications I am not aware of