You really have to watch the recommended gear feature, especially when you start melding. I don't remember the gear names, but my miner had ilvl 290 HQ gear, I acquired ivlv 340 NM gear, and it recommended I keep the 290 gear on?? what? Only after I removed the materia from the 290 gear did it recommend the 340 gear.
This has happened to me several times on different gear sets.

It would be nice to know how it decides what is "best".