Another problem that Mustrum missed, at least for me, was implementing the whole decking aspect. For that, I eventually ran with the normal hacking rules in Modern and they seemed to work OK.
You`re right, I missed that - that`s probably because that I didn`t design this part of our D20 conversion.
But in fact, I think, the whole concept of Cyberspace/Matrix doesn`t work really well - especially not in SR. The problem is everybody except the decker itself is useless in cyberspace (except maybe on those UV Hosts). Add in a complictated rule system, and the rest of the group can take a nap while the decker is getting the info.
I have to disagree with you on this one. Because of the drain rules, trolls were better spellcasters than elves!
Why? To avoid drain, you needed willpower. And it would be even better if you had good Intelligence and Willpower to have a big magic pool that would allow you to add some dice to your "will save" vs. drain. Trolls sucked at spellcasting with their -2 Intelligence and -2 Charisma...
Do I dare ask what these "flaws" are?
The general flaw is the whole d6 system. A seemingly small modifier - like a +2 - can make a commonly made task (like with a target number of 4) to an extremely difficult task (target number 6). Rolling 6 dice, you just got from an average 3 successes to 1 success. And for most tasks, you want more than one success. (that`s the reason why nearly everybody will want to use a smartgun: Targetnumber -2 for all attacks with smartweapons!)
The sheer number of dice rolled might seem fun, too, but that does only apply to the players. If you attempt to master a bigger combat with multiple NPCs, incorporating modifiers for sight, range and so on, you will get a headache assigning target numbers at one time and taking your own actions...
The shotgun rules are ridiculous as well. You can freely chose the choke - the weapons "spread" - and this allows you to hit multiple targets. This does only affect the powerniveau of the attack (the DC to reduce the damage), not the damageniveau, but it does reduce your attack rolls to effectively 2 regardles of circumstances and range. If you roll 6 dice (a typical number for a starting character in his primary skills), this means 5 success on average, not using any dice pool or other special benefits. Now, your enemy has to roll 5 success to possibly negate the attack alltogether (considering this task has a minimum DC of 4, and even a cyberupped street samurai has probalby not much more than 8 dice for this purpose). If this dodge attempt fails, he has to resist against the damage. His target number is probably 2, but he now has to roll 8 successes plus any success left from the attack to take no damage. And this was your first attack. You still have one left - and you didn´t use your own combat pool, not a burst-capable shotgun, and we didn`t account for his comrade who did also stand within the "cone of death" of your shotgun.

Well, but this problem can be handled...
Magic also has its problems: A spellcaster can always arrange to avoid any drain from spellcasting. Using most of his magic pool and having a high willpower, he only has to choose the spells to cast wisely (don´t bother with Fireball, Stunball is much more efficient...)
If you add in some bioware like the "traumadampener", you can even ignore any light drain left. Okay, this effectively reduces your magic attribute by at least one point (and you can`t do anything against it, even though bioware is claimed being less harmful to the essence and the body of a character).
Better use the remaining points of bioware you can spend wisely (maybe a Cerebralbooster for better Intelligence, or a Mnemotic Enhancer for cheaper skill increases)
Unfortunately, if you make it more difficult to resist drain, spellcasters will beomce unplayable, since this will cause damage modifiers to your target numbers, and as I said in the first part above, these numbers can make a "walk in the palk" to a "near-death experience"...
Okay, this might come as quite negative towards Shadowrun, but there are also several positive aspects -
The background is great and being a classless game makes it extremely flexible and interesting.
The game will certainly allow you to have several fun sessions of gaming - maybe you will find ways to handle the weaknesses of the game (like the shotgun rules, not all are inherent and unsolvable).
If you want to adapt the game, go for it, especially if you aren´t familiar with the current incarnation and not that accustomed to the flair set by the rules.
If you want the full Shadowrun Experience, you`ll need the 3rd edition books, no question. (You might even want them for an adaption, for ideas of spells or cyberware...)
Mustrum Ridcully