Shard Phoenix would wipe your entire board, so he's not that great. Plus, his buyback is RRR, which isn't generally a problem, but can be at times. In the list of cards you posted that hit the yard, that's 18 cards plus whatever creatures you control get nixed (+19), and Fledgling is a one-of. It shouldn't be that much of an issue.

I am also considering putting in a couple fetches to help out with that problem. I'm still not certain yet if I should, as dropping a fetch post-City then having it get Stifled is really bad.

I'd be open for more options if another creature came by, but this one is quite effective. Tutoring for Shivan is good and I've never finished a game without Thresh if I would've had the mana to cast Fledgling late game anyways.