Most obvious question first: why not puting itn on a ISA Card and take over the bus instead? Given, there would be still some work to be done after asking for DMA and pulling /MASTER, but way less than emulating a totally different CPU protocoll. More like adapting to a weired memory subsystem.
But for your points
First, most obviously, they are completely incompatible at the software level. All 286 code in ROM or on disk would have to be replaced with suitably equivalent 68000 code.
Or add a 286 emulation :)
The packages are different. The 286 is in a square package whereas the 68000 is in a DIP; something would have to be done to physically wire up the replacement chip.
Standard way would be a daughterboard anyway.
The pins are in different positions, but do they have functional equivalents? Connecting e.g. D4 on one chip to where D4 on the other was connected, would be straightforward enough, but are there pins in one that don't have an equivalent in the other?
More important, the bus protocoll is different. It will take quite some glue logic to fully emulate the Intel bus.
x86 is little-endian and 68k is big-endian. Does that matter, once you've replaced the software?
Not realy. There aren't many 16 bit ports. Beside, swaping low and hi-byte on the daughter board could solve this. But since all I/O software has to be rewritten anyway, this isn't a big deal.
Let's say for the sake of argument we are talking about 8 MHz clock speed in both cases, so that shouldn't be an issue.
Clock speed will be your least concern. It's not possible to simple tie a 68k bus to an x86 system and expect the same behaviour. Where the 68k uses AS, R/W and TACK, the 286 hardware wants to see the bus status signals S0/S1, COD/INTR and M/IO (not to mention HOLD and HOLDA and several other) Thats why every 80286 (usually) got a 82288bus controller attached. The 82288 again generated ALE, RD, WR which again are nothing the 68k generates - but the bus expects. Did I already mention the 82284 for READY, SRDY and ARDY?
What else am I missing?
What about that the 80286 got an additional I/O address space of 64 KiB? Where you want to put them within the 24 Bit 68k Address space without giving up access to some of the 80286 address space?
I don't say it's not doable, but it's definitely not just wiring up some signals - it's stitching two different components together to make them work - system design as an art form.
P.S.: This question is a bit like someone asking "To use a CPAN module in Visual Basic, wouldn't that just require aligning the parameter fields?"