The idea with rotational safeguard is that the vibration of nearby disks can throw the heads off-track. The safeguard is a sensor arrangement in the disk that detects the external vibration and compensates for it. It has nothing to do with acoustic noise. I'm not sure how much a difference it actually makes.
5400 rpm drives are a bit slower, if you install the earx into your desktop you will see speeds around 100 megabytes a second. They are of course cheaper, use less power, and run cooler. Folks here indicate the the performance drop is relatively small (maybe 10% at most).
You will see no performance boost with SATA 3. There aren't any mechanical drives that are fast enough to outpace SATA 2.
Whether 3 TB drives are worth the extra expense is an interesting question.
-On new installations, you need fewer drives to get the same space. Drives fail of course. If reliability is equal you will need fewer replacements over time if you go with fewer large drives. Since 3TB prices are dropping this could save you money in the long run. Also, if you leave a spare slot then you can add capacity without needing to discard/re-purpose a working smaller drive.
-On upgrades, once the chassis is full your only option is to replace a smaller drive with a larger drive. If you have 1 TB drives today, it is already about the same cost (per added gigabyte) to upgrade to 3 TB instead of 2 TB. If you have 1.5 TB drives today, it is actually cheaper (per added gigabyte) to upgrade to 3 TB.
Overall, I figure its a wash today with the cost advantage shifting to 3 TB soon. With my pro 6, I had four 1.5 TB drives already in hand, I augmented that with 2 3TB drives. (The 3TB are 5400 rpm btw). As the 1.5 TB drives age, I'll replace them with 3 TB.