Interesting.
You're not the first person I've heard this from, but at the same time, it makes me think that the guitars with passives you've used, weren't that great of a guitar to begin with. You can throw EMGs in a cheap guitar, and it will sound great, because they tend to have a certain character to them that relies less on the guitar's quality. Doing the same with passives will show more of the guitar, and it will be clear whether you're using a cheap guitar or not.
I'd challenge you to try out EMGs in a fairly high end guitar vs. a set of nice passives, and see if you still prefer the EMGs. Having A/B'd a set of EMG 81/60, BKP Nailbombs and Duncan JB/59 in my Jackson SL2H, there's no doubt in my mind that the passives were tighter and clearer. Not as "big" sounding, no, but the difference was so profound that I will only ever use EMGs on heavy rhythms for my own stuff anymore. There's just something about EMGs that makes palm mutes sound even and less dynamic, I've heard clips of them where it almost sounded like the person was using a completely different technique on mutes than on the passive pickup version. Passives always sound more lively and crunchy on palm mutes. They have a grind to them that makes them sound less mechanical and "real" for lack of a better term.