The linear nature of grappling in this game has screwed up people's perception of "in real life" arguments.
The first point is interesting, and probably a good idea for the game. That being, make it more difficult to obtain the crucifix position in the first place.
In reality, getting there isn't really a case simply going through positions until reaching side saddle. The side saddle allows for more control, but limits options for the top player. I'd also argue side control is better for getting to crucifix, but not the point of this discussion. More important to this point of making it a more difficult position to attain, there could also be an element of needing help from the bottom fighter in order to get there with more ease (a bad escape attempt, or if there were more options for defense from the bottom it would offer more options).
In the meantime, I think it would make sense to have wider variance in how statistics like ratings, jiu-jitsu and/or wrestling level play into this. A good grappler is unlikely to give up that arm (and they sure as hell know from side saddle). On the flip side, there should be wider dispersion between fighters skills that determine the ease of getting the position - and, again, a wider gap in ability to hold the position.
All that aside...
I think Solid nailed it, as far as the reason for the current mechanics. Makes sense that the developers simply had to find ways to create artificial barriers created by the linear grappling engine. I assume that, because crucifix is so strong in this game (and so damn easy to attain), they forced the circuit of: Side Control -> Crucifix -> Side Saddle... to allow more opportunities to block being put back in the position after an escape.