I am not sure if a D20 version would be the best way, but the d6 version is flawed.
Many of these flaws are because some of the designer often seem incapable of seeing how the rules can interact with each other and unbalance certain aspects.
But one major flaw is the d6 mechanic.
I liked the base idea - using number of successes to determine the effect of a task, and having a variable DC. But actually, the variation you can make on a d6 isn´t that great - a modifier of +2 can make a task from simply done to impossible. This does also result in increasing the lethality, sure (if you have a moderate wound, you can go home...).
From a d20 perspective, the smartgun is to a street samurai as a +5 enhancement bonus to a fighter.
Combats in d6 are extremely long. You roll an attack, the defender rolls his dodge roll, you determine success, the defender makes his constitution roll.
And if you use all of the combat modifiers (which is appearently expected from a reasonably intelligent, er dedicated Shadowrun player), you have to consult a few tables before even announcing the DC. (And you will be surprised how high it will be if you use all the modifiers!)
Spellcasting in d6 is one of the hardest thing to apply to D20 Modern.
But I don´t think the d6 rules are really balanced here. The few spells that are essential to a deadly wizard can be acquired at the beginning. Drain will never become a real problem, especially if you add in some bioware equipment (trauma dampener would be the wet dream of every spellcaster, if it wouldn´t already exist
).
Another problem is character development.
It will take a long time to advance a skill, learn a new spell or improve an ability score.
But on the other hand, most runs will get you so much money that you can easily improve yourself by buying armor, cyberware, vehicles or weapons.
(And this is the point where it suddenly sucks to play a spellcaster - you will take forever to improve your abilities, because every improvement requires money AND karma).
The designers seem to have encounted the same problems as we (we as in our group or we as in all Shadowrun players around the world
) do, and are then creating new equipment/rules to work against it.
Damage Compensators to avoid damage modifiers, talent softs to avoid slow skill advancement, Anti Vehicle ammunition to fight against the overarmored rigger drones. Unfortunately, most of these changes are flawed - they don´t fix the problem, they make other abilities worthless (why learn a skill? get skillwires on level 8, and than shop for the skills you need), or are very unreasonable ("Wow, this cool antivehicle ammunition halves the effective armor rating and negates the damage penalty? It must be overkill to shoot at unarmored people with it." - "Nope. Same effect..).
There are even other, minor flaws in the system (but shed a bad light on the game designers):
People in Shadowrun have a reasonable chance to die from a fall from 2m, and are probably severely injured after it. (3 consitutition die against 2T damage?)
The security distance from exploding antitank missile varies between 2 to 4 meters...
Some Antiaircraft missiles deal more damage if the target is in air...
Shotguns are the ultimate weapons of destruction...
(Hmm. My hat of 6d know no limit?
)
But back to a conversion:
I think you can easily increase the lethality of D20 Modern - the Massive Damage Threshold is the only tool you need. Set it at a static 10, and add one at 20 with a higher fortitude save to resist, and D20 Modern is extremely lethal ...
I think the main question is not if the Shadowrun rules are bad, the main question is how to improve them - a d20 conversion isn´t probably the easiest or best route, but I think it is a viable one.