Nice system possibilities. Upgrading the OS is probably the next logical step, but, it can be complicated on the 2000. You can install a newer kickstart rom on the motherboard. You may, however, need to also upgrade the rom chip on the card you choose to drive your SCSI harddrive and CDrom to get the system to boot. This additional rom is not usually expensive. There are ppl here who remember the specifics of this better than me.
OS3.9 was designed for higher spec Amigas (those with 32-bit acceleration, some fast ram, and especially, retargetable graphics, required for the non-standard icon display engine). Adding a Picasso II graphics card (especially true as you already have a flicker fixer) would also be a logical upgrade for your system to make all of this work and a real sweet system. That said, there seems to be many ppl here who have run 3.9 with ECS standard graphics (and older 16-bit CPUs and fast ram). I don't know how they did it, but I think it was labor intensive to replace all the icons.
Your system, as it's currently configured, might be ideally suited to OS3.1, many ppl believe it the most pure choice, anyway. It can be enhanced and tweaked with selected elements of 3.9 (and 3.5). Operating Sytem3.1, OS3.5, and OS3.9 work well with, and need, kickstart rom 3.1 installed on the motherboard.