"3rd ed has lots of bad rules"
Paraphrased.
So I think reworking the system was really necessary.
The system definitely was not great, good or even ok.
All that being said, I really liked to PLAY shadowrun.
Completely agree in basically every way. The most fun paper and pencil RPG sessions I've played were SR games even if they system is not up to snuff.
In fact, we played SR for 2 weeks when people in the group left early - everyone had so much fun that we are, in fact, going to keep playing SR instead of D&D in our "off main campaign" slot.
The thing is the basic system works fine and that is what I use. The basic system is very fast and intuitive.
The basic system does not really need an overhaul. When I describe basic system I mean...
Roll a million d6's and see how many 4+ you got, compare them to how many your opponent got. Repeat.
For NPCs I simply used "ratings". Rating 5 NPCs had 5 in everyone, Rating 6's had a 6 in everything and so on. This allowed for infinite scalability and extremely easy pre-made NPCs. A rating 4 mage is not that scary (force 4 spells are a joke), a rating 6 mage is godly.
But yes, as you added layers of complexity on top of the simple rules of the game things broke down but they do in every system. At the heart of the d20 system is rolling 1d20, adding modifiers and checking the result - and it's a perfectly playable basic system. It runs into the same problems with a million modifiers and so on "getting in the way" of the ease of the system for more "flavor".
For the record, I've never had problems with Magic in Shadowrun or Riggers or Street Sams or Adepts. I find that a gentleman's agreement between GM and players has been enough to nix pretty much all problems.
Take your ambush scenario. If you were to prepare an ambush versus your players in exactly the same way they would have been just as boned as the large convoy. Anytime a PC fires their sniper rifle and kills someone from 2 miles away I remind them that, one day, the same exact thing could happen to them. I keep track of things like that: "Negative Karma". Accumulate enough Negative Karma and they will catch that sniper's bullet one day. That's exactly how the game world works.
I've only ever had problems with Deckers and I did the simplest thing I could to fix that; condense 30+ pages of decking rules into a Computer roll and static DCs vs. deck ratings - with lots of RPing and fewer rolls. Results have always been good there. Decking is definitely the clunkiest and worst aspect of the game in terms of rules and I don't know any group that after playing for a while continues to use the base rules there. Everything else, combat/rigging/magic are solid enough (not perfect, not great, not good but okay) so that with a few tweaks here and there with a lot of emphasis on the basic system of the game it has always worked out well enough for me.
YMWV