I was involved in chipset testing. One of the prominent examples where ISA transactions simply cannot be translated to properly formed PCI transactions is in the case of ISA DMA. There is no correct mapping possible -- the timing requirements on the ISA side are "hard" and the PCI bus doesn't have the needed transaction types to fully support ISA-side DMA without the sideband. So the Intel chipsets all (up to the point where I stopped working with them directly, anyway) included pins which were simply called "sideband." These pins couple the southbridge with the main chipset in order to inform it about things like ISA DMA, which have to be handled through PCI transactions but where the timing requirements are hard and the chipset needs to support them. This was necessary as PCI transactions had to be "twisted" a bit to make this work.
This is what I mean by sideband -- these out-of-band communications between the southbridge and the main chipset for support of things like ISA DMA timing.
It was these sideband channels that accounted for about 1/2 of all chipset bugs, so I know these sidebands exist. Plus, of course, I had to read the data sheets and understand things like the inbound and outbound queuing, read around writes, and a host of things regarding testing the chipsets with FPGA boards on both sides of the southbridge, trying to break it.
Like I said, things may have changed. It's possible that I'd barely recognize the PCI, today (though I doubt things have changed that much.) But I don't yet see how ISA DMA timing, for one example, can be maintained exclusively through standard PCI transactions and without any "extra communication" to the chipset.
I'm not saying that a reduced ISA wouldn't work -- it would. But there are a few bits of non-overlapping semantics between ISA and PCI. And these are usually handled by the sideband channel. I can assure you that if Intel could have gotten rid of it, they would have clawed and screamed to do so. It was a sink of engineering labor they would have been glad to be rid of.