Some of those are less-connected than others. Repairs, so far, has not really been connected. 0-8-4 is sort of the same way, although it was laying the groundwork for basic SHIELD procedure and terms, so I think that ones more forgivable. Also, there was an ongoing plot arc of Skye at the time, which was important for The Asset and Girl in the Flower Dress. I think that plot wasn't so great, but it was, even early on, an attempt at a mini-ongoing plot. However, if the criticism is "90s style episodic," I think even 90s shows had ongoing character arcs, so I'm not counting Repairs as favorably (The Well's establishment of May and Ward's relationship is a little bit stronger, though).
That being said, if the reference to Roxxon Corp in Repairs wasn't a throwaway reference (it appeared silently on a newspaper or something like that), I'm not convinced that episode was so standalone. After all, CyberTek and Deathlok are affiliated with Roxxon.