I just installed a 6 Gbps SATA III [https://www.sandisk.com/home/ssd/ssd-plus|Sandisk SSD Plus] in my [http://www.everymac.com/systems/apple/mac_mini/specs/mac-mini-core-2-duo-2.26-late-2009-specs.html|late 2009 Mac Mini] (running El Capitan) and was dismayed to find it operating at a negotiated link speed of 1.5 Gbps. I found a [http://forums.sandisk.com/t5/SanDisk-Extreme-SSD-Legacy/Macbook-Pro-Link-Speed-1-5G-instead-3G/td-p/276288|discussion thread] from 2012 on the Sandisk Forums isolating the issue to a finicky NVidia MCP79 SATA chipset on Macs of that era and suggesting going with other drive manufacturers; I also found that Sandisk had acknowledged the problem and had released a [http://kb.sandisk.com/app/answers/detail/a_id/12314/~/sandisk-extreme-ssd-manual-firmware-update-version-r211m-%28mac-with-sata-link|firmware patch] specifically for drives in Macs with the MCP79 chipset, albeit only for the Sandisk Extreme SSD. I figured I'd try the patch on the SSD Plus anyway (and return it to Amazon if it failed), so I burned the ISO to CD and tried to boot it off my external USB Panasonic DVD burner (the internal Superdrive has been dead for years). Unfortunately, the Linux system failed during bootup, so I rebooted to the SSD. To my surprise, I found the link operating at 3 Gbps.
I had no illusions that the failed firmware loader had miraculously updated the firmware, but I found it curious that the link would be at 3 Gbps after trying to boot from the CD. I ejected the CD and restarted the Mini, only to find it back at 1.5 Gbps. I put the CD back in and rebooted to the SSD, and the link was back at 3 Gbps. Even after several restarts it stayed at 3 Gbps, as long as the CD was in the drive. Then without the CD in the drive I tried running [https://support.apple.com/en-us/HT204417|Startup Manager] at boot (by holding down the Option key) and selecting the SSD, and the link was at 3 Gbps. I can now repeatably and reliably get the link to run at 1.5 Gbps or 3 Gbps, depending on how I boot the Mini to the SSD.
Based on my observables, I would isolate the finickyness of the NVidia MCP79 chipset to a timing issue at boot—if you allow the startup to occur normally, the link negotiation will fall back to 1.5 Gbps. If you instead interfere with the startup, say by having a CD in the drive or by running Startup Manager, the link will negotiate to 3 Gbps. I'd be curious to hear how other SSDs fare with this solution; I'd also be interested in whether the CD solution works on an internal Superdrive.