Adding/removing instructions isn't going to fragment, added instructions can be ignored (see the 68020) and removed instructions can be trapped (see the 68060)... Fragmentation would occur if instruction behaviour is altered...
Reusing a previously assigned opcode cold cause problems, unless it wasn't commonly used on the Amiga... If it has potential to improve compiler code generation, or speed execution... then I say go for it!! 
I disagree. If instructions are added, then software will be written that uses them (you'll need a new compiler as well) and every other CPU will not run the software properly.
It's like the Microsoft embrace and extend tactic. Be compatible, then add just a little change that people want to use. Pretty soon others are obsolete and incompatible.
Higher speeds are great, but we can't afford more fragmentation. It's just not worth a few clocks in specific situations when we can use more efficient hardware/firmware. We're in the age of multi-GHz parts, we can get massive performance increases without resorting to a new instruction set.
If instructions are removed, but you include efficient traps with your hardware, that's fine but awkward for the user. I absolutely hate dealing with 060 libraries.