It really all depends on the goal you set for yourself. If you want to run as many games as possible in a single build, Pentium 3-era hardware with an ISA is the best option. If you want to run ALL games in MAXIMUM quality, then you will not get away from building MANY builds: in those days there were no generally accepted standards, games were often programmed tied to a specific hardware. There are so many challenges that you will have to overcome:
1. DOS games need sound. There are many standards, many synthesis implementations, many sound cards, but none of them can provide 100% compatibility and quality. You will need several cards and even several builds. ISA slots can help you a lot but generally ISA cards are also noisy and can't provide digital output like later PCI cards.
2. If you are interested in DOS, then you need to consider the compatibility of your video card. None of them are 100% compatible. Also later cards may have problems with performance in DOS.
3. To play early DOS CGA games with artifact colors, you not only need a compatible card, but also a composite monitor.
4. Speed sensitivity existed right up until the early 2000s. Late games are less affected, but still. Slowing down the processor is not such a difficult task, but not all slowdown methods ensure smooth and glitch-free gaming. Sometimes theory differs from practice.
5. There were several APIs for 3d rendering. Some games look better on one and some look better on the other. In addition to the objective difference, there is an individual perception (some people like software rendering, some like Voodoo, and some like Matrox Mystic).
6. Sometimes drivers break compatibility or stability, even if the hardware itself has no problems. For example late GeForce drivers for Windows 98.
7. Small nuances like stars in Thief 2 or fonts in NFS Porsche Unleashed.
8. Latest games compatible with Windows 9x not only work in Windows 2000 or XP, but can also take advantage of the dual-threading capabilities of a Pentium 4 with hyperthreading, Pentium D and Core 2, even if the video card is the same. You must decide where your borders of the 9x era will be.
9. Windows 98 without hacks has problems with memory greater than 512 MB. At the same time, later games compatible with 98 may require more. Millennium works fine with 1 GB, but it has more problems with DOS.
10. If your goal is to also cover Windows 3.1 or OS/2, then you will also have to select hardware compatible with them.
11. Older games definitely need a CRT monitor to look right. However, newer games can take advantage of the digital output and look great at the quality LCD monitor's native resolution.
12. There are differences in dithering and antialiasing between different video cards. Some may look better, but work slower or be less compatible.
Compromises, compromises, compromises... They will always be there. Only you decide which ones you are ready to accept. Collecting 10 assemblies for retro games is also a compromise. You need space for them, money and time to maintain them. Using of software and hardware emulators, different adapters, modern retro hardware replicas, wrappers, unofficial patches can help you a lot but it's still a compromise.
As a conclusion: fast ISA-less builds compatible with Windows 98 have their niche: they run a significant part of games from the late 90s - early 2000s in maximum quality. No more no less. For someone, this may be the main everyday build. An important advantage will be the greater reliability and simplicity of this hardware compared to older ones. For some, such build may be pointless at all.
