I realize to do not post much on this forum, so feel free to take my opinions lightly. I find the Civic SI to be a fun little machine to drive. I was almost just about to toss the money down for one until the Mazdaspeed 3 came out. To me, the Civic improved on everything the early 2000 model sport hatches attempted to achieve short of the SRT-4's power advantage. The Civic SI certainly still causes me to turn an eye for a look though.
Regarding the motor mount issues. In most cases, at least from the front wheel segment, it seems that they will be softer from stock due to NVH protocol. Unfortunately, very few people would probably jump at the chance to buy a car that rattles or vibrates at idle due to a stiff performance mount. We should all know by now that performance minded individuals are not the only ones that shell out money for performance cars. At the same time, I don't think the ratio of performance minded individuals to more naive individuals (with regards to the automotive subject) is that great in the grand scheme of things. Take this information for what you want, but I recall some SRT-4 owners complaining or motor mount issues as well as similar issues with my SVT focus. It may just be an overall issue with front wheel powered vehicles, when NVH plays a higher priority.
With regards to the 3rd gear transmission issues in the first run of the SI, I was slightly surprised and at the same time not so once I thought a little more about it. I don't recall Civic SI's in the past having such mechanical issues. I do vaguely recall however from visits to Acura forums back in the day, of transmission issues with several performance variants like the Type-S RSX and TL's. I don't know what to make of that there. Some cars will have issues in any model run and some won't. It's the nature of the consumer world. The SVT focus was known for flywheels/clutch combos failing due to an improper set up. I never had that problem, but I know another person who bought another SVT at my same dealership the same model year, had the problem and many dealer visits. The only issue I ever had was a loose heat shield at the catalytic converter that created a rattling noise and minor squeaking from the rear suspension when there are no load (people/luggage) on it. I've also have had no issues with my MS3 short of the recall cell from the shutter valve, so I would suppose I'm lucky again which was promptly corrected under warranty.
Lastly, I would like to provide an opinion on the interior differences I've noticed in both the 3 and the SI. At first glance, I thought the Civic was superior in interior fit and finish, but notice that the plastics used for the interior dash did not look as good as the 3 in some parts. With that in mind, I find the dash to be of better finish to be in the 3, while the center console seems of better fit in the Civic. To those that prefer the hideaway cup holders on the 3's console, they will be more pleased obviously by the 3. The Civic I saw did not have that, if I am mistaken in that respect. The gauge instruments on both cars are hit or miss with preference. I really like the Civic's digital gauges as they seem more in place with concept car applications and it's certainly refreshing to see in this car segment. The 3's interior gauges are also top quality in my opinion as well, but certainly more analog in appearance. What I'm really trying to get at is that you cannot make the same comparison between these 2 cars in interior finish than if you were to compare either car to a US model variant within the same car segment. This would would be an obvious plus for both of these cars.
I would hope my insight helps anyone trying to decide between these 2 vehicles.