On the fist matter, I recommend considering the alternate rule explained on page 75 of the Shadowrun 20th Anniversary core rulebook - instead of rolling the Damage Resistance test, you simply subtract the armor value from the damage done. It keeps things moving pretty fast by cutting down on rolls, but it does make it a little harder to cause damage to heavily armored characters.
As for the idea of an indestructable Orc with 16 dice for damage resistance... a shot from a heavy pistol, an Ares Predator IV for example, has a minimum 6 damage value for a successful attack, meaning that a target would need around 18 dice to regularly shrug off the damage or have some seriously good luck with his dice. Wounds add up, even the little ones, as every 3 damage results in a wound penalty that drives their dice pools to avoid getting shot towards zero - and with multiple shots against them the defense drops as well, and burst fire or full-auto can reduce that defense even further.
Your "indestructable" Orc could end up having a character shooting and SMG at him in two short burst per Initiative Phase, which would mean his first Reaction roll would be at -2 (because of the wide burst rules) and his Reaction roll to avoid the second burst would be at -3 (2 penalty from wide burst + 1 penalty from being attacked more than once). If you have more than one shooter, you quickly have an Orc with no defense at all against incoming damage other than to roll Damage resistance.
For Initiative Passes, it seems like you are saying that you think a guy with 3 Initiative passes gets all 3 of them at the same time, and that is incorrect - everyone gets to take their turn once no matter how many initiative passes, then those that have 2 passes take another turn, then those with 3 passes take another turn, and so on all in order of their Initiative rolls.
If you had that right and still don't really like what it does (which I personally don't like it either), here is a house-rule I use that is basically lifted from Shadowrun 2nd Edition:
-Leave all the augmentations as they are in the book, and change nothing about the character sheet.
-When rolling initiative, instead of rolling dice equal to the initiative score of the character, roll a number of dice equal to the character's Initiative Passes and total the result (pip or number total, not number of hits).
-Add the character's Initiative Attribute to the total rolled. That is when the character takes their first action.
-Subtract 10 from each character's initiative roll, if they number is 1 or greater that character also acts on that initiative.
-Subtract 10 from each of those results, characters that still have a 1 or greater number act again on that initiative, repeat that process until no one has a number 1 or greater remaining or the character has a total of 4 times that they act.
-Re-roll each round.
To put that example in practice, let's say you have a wired guy with 3 Initiative Passes and an 11 Initiative score, a completely average guy with 1 Pass and a 6 Initiative Score, and 3 goons with 2 Passes and 8 for their Initiative score.
Their Rolls would be 3d6+11, 1d6+6, and 2d6+8 respectively. Let's say those rolls come out as 19 (2+2+4+11), 12 (6+6), and the 3 goons get 10 (1+1+8), 20 (6+6+8) and 15 (3+4+8), you would then have an initiative list that looks like this
20 - Goon 2
19 - Wired Guy
15 - Goon 3
12 - average Guy
10 - Goon 1 and Goon 2 for the 2nd time
9 - Wired Guy for the 2nd time
5 - Goon 3 for the 2nd time
2 - Average guy for the 2nd time
Then re-roll.
The rule makes it so that people without reflex boosters have a chance to act more often, and so that characters with maxed-out reflex boosters are not as likely to get as many actions - evening the playing field and making reflex boosting magic or augmentation less important overall.