Really? I remember it having a "chiclet" keyboard that was widely criticized among other things. As for the compatibility, I'm not sure how many computer makers at that time--including IBM--completely grokked that PC compatibility really did mean 100% compatibility as opposed to mostly compatible.
For the home market where the Jr. was aimed it really needed the better graphics and sound to compete with the C64 and the like.
But to your basic point. Yeah. IBM wanted to create a competitor to the other home computers. Not cannibalizing its business computers was probably a rather secondary concern.
I'm sure the PCjr could have really taken off if it had been more like the Amiga.
The PCjr had the promise of "runs some PC software", so if Dad needs to finish his spreadsheet from the office in an emergency, he can barge the kids off the PCjr for the night.
If it had been something different to the point of total incompatibility, why not buy the kids a cheaper Atari 800XL or C64 for games and "educational software" instead?
You can also argue that the PCjr's unique features did survive a bit longer, in the form of the Tandy 1000 series.