And getting a PC Case without enough slots is incredibly easy to do.
EG. we need lots of USB ports these days -  can be all of printer + keyboard + mouse +external backup drive + external audio speaker system.

Bigger fan(s) mean quieter PCs ( I've read somewhere).
There are full height and half-height slots, full and half-height hard disks.

When you get a configuration, post it here and then maybe svdl or another expert will make a detailed recommendation you can proceed with,
whether you build it yourself or order a custom-made one.