Just to give people an update on current cases. Here are the ones I found that I liked the most, there are others of course, but I thought I'd point out the ones that really have good capacity and are actively being sold right now rather than discontinued as of this posting date.
Fractal
Define 7 XL series - Full Tower: https://www.fractal-design.com/products/cases/define/define-7-xl/Black/ 18 3.5" drive bays with add on HDD cages $200
Mesh 2 XL Same case as Define 7 XL, slightly different airflow, Mesh 2 XL - Full Tower: https://www.fractal-design.com/products/cases/meshify/meshify-2-xl-dark-tempered-glass/black/ ~$200
Phanteks
Enthos Elite - Super Tower: https://phanteks.com/Enthoo-Elite.html -13 x 3.5" and 6 x 2.5" ~$850
Enthos 719 - Full Tower: https://phanteks.com/Enthoo-719.html 12 x 3.5" and 11 x 2.5" ~$190 I have this case and REALLY like all aspects of it, from water cooling, lighting, build quality etc
Enthos Pro 2 - Full Tower: https://phanteks.com/Enthoo-Pro2-TemperedGlass.html - with extra drive trays 12 x 3.5" and 3 x 2.5" ~$190 I have this case and again really like it, but the Enthos 719 is better
Eclipse P600S - Mid Tower https://phanteks.com/Eclipse-P600s.html 10 x 3.5" and 3 x 2.5" ~$160
Eclipse P500A - Mid Tower https://phanteks.com/Eclipse-P500A.html 10 x 3.5"
Corsair
Obsidian 750D - Full Tower https://www.corsair.com/us/en/Categories/Products/Cases/Obsidian-Series™-750D-Airflow-Edition-Full-Tower-ATX-Case/p/CC-9011078 9 x 3.5" and 4 x 2.5" ~$160
Obsidian 800D - Full Tower https://www.corsair.com/us/en/Categories/Products/Cases/Obsidian-Series™-800D-Full-Tower-Case/p/CC800DW 9 x 3.5"" and 2 x 2.5" ~$300
Obsidian 1000D - Super Tower https://www.corsair.com/us/en/Categories/Products/Cases/Software-Control-and-Monitoring-Cases/Obsidian-Series-1000D-Super-Tower-Case/p/CC-9011148-WW - 5 x 3.5" and 6 x 2.5" $500 I also own this case and it's a beast, I do love it, and it's stuffed with equipment and water cooling. Given how much space there is, you can easily add extra 3.5" (12 or 25 more easily) mounts, just not sure it'll be pretty.
Thermaltake
View 91 RGB Plus - Super/Full Tower: https://www.thermaltakeusa.com/view-91-tempered-glass-rgb-edition.html 12 x 3.5" or 2.5" ~$500 (just ordered and will see what the quality is like and looks like lots of space for what cooling too)
Level 20 - Full Tower https://www.thermaltakeusa.com/level20.html 14 x 3.5" or 2.5" $1000
Core W200 - Super Cube https://www.thermaltakeusa.com/core-w200.html 17 x 3.5" or 2.5" $550 (dual server case) expandable
Core W100 - Full Tower https://www.thermaltakeusa.com/core-w100.html 13 x 3.5" or 2.5" $400