There were some innovative large-OEM PC designs in the mid-late 1990s, e.g. the IBM Aptiva S series, some NEC models, etc. They were also extremely pricy.
The problem with these machines, really, is that they were expensive and had mediocre internals. Likeliest market would have been higher-income families wanting a computer for the kids and not knowing much about the details. As the kids got older, as information about what components are good/not so good became more plentiful, and as computer lifecycles shortened, the market for those machines plunged.
The more demanding, more knowledgeable, higher-spending customers went to Dell/Gateway, the clone shop down the street, or started building their own machines. And for them, if anything, modularity was more important than design. Stuff was moving extremely quickly, the large OEMs had way more compromises on expandability, and many people had been burned by their previous large OEM system having woefully inadequate expansion (e.g. my early-1995 AST system with a single PATA channel, 8250 UARTs on the external serial ports, a generic parallel port, one free ISA slot, soldered video, and a 528 meg BIOS hard drive limit when the machine shipped with a 420 meg)
Everybody who remained, well, became increasingly price conscious. As the price point of large-retailer Windows system plunged in the early 2000s, any willingness to experiment on the high end with design plunged with it. Except maybe a little bit with Sony Vaios. And this continues to this day - high-end non-gaming non-businessy Windows laptops have struggled whereas Apple sells MacBooks at those or higher price points all day long.