Soccer has been around a long time and has an incredible amount of tradition. Like any sport, there are lots of rules that could use alteration but it is tough because the sport is worldwide and it is old.
But anyone pretending that American Footballs system of marking where a guy goes down, and then bringing out chains to measure to the inch for a first down is somehow a good system that couldn't be improved is either crazy or blind. Or pass interference rule. Or the strike zone in baseball. My point is that it is the same for every sport.
But to address some of the biggest complaints...
First the 3 sub rule. It is in place to protect the smaller teams with smaller budgets. Unlimited or increased subs mean that rich teams that can essentially afford 2 full starting teams would have a massive advantage. Smaller teams can barely afford a starting 11 of decent quality and would never be able to compete against a bigger club who could bring in a fresh second team.
The clock, the fake injuries, the time wasting.... I also agree that this is a big problem that is easily solved. Don't keep a secret clock on the sideline, let there be a clock that counts up from zero that starts the second there is a stoppage. It is for everyone to see. So when someone goes down with an injury - who cares - you can see the time being added - let him roll around for as long as he wants. This will stop this type of behavior - along with the walking when subs are made - and other time wasting BS. But once again, tradition is the biggest obstacle to this - but I do see this changing one day.
Fouls in the box. PK's are too valuable for a simple foul in the box. I am open to suggestions on this one - but I think that you keep the foul in the box as a penalty - but you have a simple review when penalties are called. There is a natural break of time when a penalty is called - and a simple video review with a "yes" or "no" is relayed electronically to the ref. If it is a dive, a yellow is issued. If it is a penalty, the PK is awarded. Either way - no extra time is needed.
But overall - none of these things ruin the sport for me - and the thought that the sport needs to be tailored to Americans is just silly. Show me one sport that doesn't have these similar problems and slowness to move. Soccer is clearly slow and very intrenched in tradition - and FIFA is a corrupt old boy network - but overall I find it much more tolerable than most sports.