Are you using Beamer? What CTAN packages are you using? Those long render times could have quite a few reasons but fonts are one reason for sure.
If you want absolutely instantaneous (on the order of ~100ms for full generation of entire thesis with multiple passes for TOC/index/list of figures proper enumeration) output, RAMdisks with all of your content - that means install, fonts, graphic assets, packages, etc is only the way to go (without re-writing large chunks of LuaTeX). When I needed a quick render loop for final alterations, I had ~6gb of RAM on a dedicated partition in /opt/tex/ on FreeBSD setup just for that and it was nothing short of a pleasure.