The thing with SR 5e rules is that for most part they _actually_ work

They are crazy, but they do work and have their own internal logic that does sorta make sense once you get used to it. I have ran a bunch of games in SR5 and once you let go of your initial fear of the daunting system and embrace it its not bad at all.
The "three parallel worlds" issue is very real. You can go two ways here:
1) Impose limitations to reduce the complexity (e.g. "no deckers", "no astral projection"). This is the easiest way, but imo takes away some of the uniqueness of the shadowrun experience
2) Embrace the madness and just run with it. This requires high level of command over the rules and a very high degree of parallel computing by the GM, but if you do pull it off it does add to the game. Deckers hacking on the fly while bullets are spraying all over the place and the shaman battling it out in astral space against approaching spirits IS the heart and soul of shadowrunning IMHO.
One ting I really like about SR5 is the initiativ system and generally the combat rules. One of my players (who are VERY picky about rules) once said "when we fight in shadowrun I really FEEL like I am in combat for real! Its fast, furious and messy and I have NO idea what is going to happen next!". For me this is ultimate praise for a rule set in fact.
So, in summary, SR5 is a HELLISH system to GM. But it is ultimately quite rewarding. When it runs it flies.