What is an SSD drive's negotiated link speed?
Solution 1:
Yes - at the moment - those link speeds are the theoretical maximum speed at which data can transfer to or from those devices.
The EFI firmware version on your MacBook Pro controls these link speeds as well as many other aspects of CPU throttling, so without reverse engineering that code - it's hard to know what or why the link may re-negotiate at a different speed. In the past, Apple has released EFI firmware updates to increase SATA link speeds for third party drives when they have done the engineering to make sure it will be stable enough - even if they don't support those drives. Of course they also release updates to improve their OEM parts in terms of speed and reliability so you can monitor those link speeds as well as your actual bottlenecks and submit bug reports if you feel things are not optimally configured - especially if you have some benchmarks or other data to show that case.
Solution 2:
In this case: The Toshiba TS256C is operating at its fastest factory designed speed. Basically, you bought an Apple computer with an SATA III (6Gbps) interface and an SATA II (3Gbps) Hard Drive, and an SATA I (1.5Gbps) optical drive. If you were to buy a different model of SSD or ODD that is SATA III rated for speed you could take advantage of the 6 Gbps speeds on either interface.
Apple has been known by the spec tracking community to do this for various models since around the time they introduced SSD's. It's a silly thing to do for a company that only officially supports a couple of after market internal hardware upgrades, basically limited to Crucial branded memory, AFAIK. Why they cripple their machines this way is probably a business decision: it's cheaper and most consumers won't ever know/figure it out/be able to tell.
Solution 3:
I have a mid-2012 (unibody, non-Retina) MacBook Pro 13" that I retrofitted with an OWC Mercury Electra 6G SSD, and my System Profiler reports
Link Speed: 6 Gigabit
Negotiated Link Speed: 6 Gigabit
So perhaps mine is faster than the OEM drive in your MacBook Pro.