EM Joker Poker also only has a double bonus as opposed to the 5x bonus the SS game has, presumably to keep scores lower since the EM only goes to 199,990.
I own an EM Cleopatra, and I've played SS Cleopatras at shows. Some takeaways I've noticed, is that they have identical gameplay feels. All the coils and flippers between the EM and SS versions during this time were DC driven. However, the EM version is slightly slower, simply because it had to tally scores, and the "scanning bonus" Gottlieb loved using moves much faster in the SS version, since it would intelligently skip non matches.
So I guess it would really boil down to personal preference. I know if it were me, I'd take the EM version all day. They're not different enough for me to really notice a difference, and the EMs are just super cool and alluring.