As far as integrating GFX/Audio w/ DMA on the motherboard, even most modern x86 boards do this, with a bypass ability to upgrade, which the Amiga didn't really have. (At the OS level, it did, but lots of "hardware banging" programs can't access enhanced GFX without the card doing wierd things, eg. I still need a VGA switch + scandoubler to play WHDload stuff) As far as proprietary GFX (eg. OCS/ECS/AGA being planar instead of chunky), API layers seem to make up the difference a bit, but the Classic systems are conceptually incompatible with the way other systems do it on a more specific level. But the overall concept is still sound, the only problem being with upgrading. The only problems I've had getting my A1200 towered and operating in a "modern" capacity, aside from cost, are the "fixed" nature of the custom hardware. While I still need AGA (in my case) for games and older software (DPIV can use RTG, but doesn't really like it), upgrading past the original specs. is a challenge when you have "native" hardware to bypass. The biggest prob is the KS ROMS, which I believe most OS4.x systems have opted for a system more similar to BIOS rather than kickstart, though I could be wrong. (Haven't had the pleasure of tinkering with an A1 or SAM, etc..) I use AOS 3.9, which required me to disassemble my 1200, swap out the 2 chips, and then run a ROM patcher on top of that. Been thinking of finding someone with a ROM burner and seeing if I can't bypass the whole boot, blizkick 3.9 rom, reboot process. If the ROMs are flashable, or more like NVRAM, it may be more convenient, and give the best of both worlds. (I know many x86 boards have flashable bios chips)
The biggest drawback to "Amiga" arcitecture (as I know it, the 680x0 based systems) is lack of expandability of the GFX/Audio in a more modular method, but between the flashable ROMs and less software being written to hardware (even windows has a hardware abstraction layer to code to rather than the CPU, would be interesting to see what would happen if HAL.DLL was ported to 6800x0 architecture) the Amiga's can (and does, considering lack of realization of an "apples to oranges comparison between kickstart and bios) model work.
Sorry if I'm a bit wordy on this post, the next task on my agenda for today involvles changing a cat litter box, when I live with 3 cats that apparently don't agree with the brand of cat food I recently bought.