The salient difference between fairy Flight and the Fly spell is the spell requires the concentration mechanic. To fly without concentration, so as to add other magical effects, can situationally be extra powerful. Fly is the kind of spell that kinda deserves concentration, so as to avoid stacking. Also, the spell only lasts for 10 minutes.
Until now, I have been expecting players to gain flight in terms of tiers.
Levels of Tier: Flight
• 1-4 Apprentice: limited forms of flight (Levitation, Spider Climb)
• 5-8 Professional: temporary access to perfect flight (Fly)
• 9-12 Master: permanent perfect flight is usually normal by now
So, for me, the fairy Flight trait is making a mid-tier capability available at level 1. For me, this is shocking.
However, the designers a fully aware of how powerful flight is − and they have a history of nerfing overpowered abilities. I take this to mean they are intentionally making flight a normal part of gameplay.
Compare Invisibility: also potentially ultrapowerful, but is a normal part of D&D gameplay.
Capabilities that were overestimated but are now becoming more normal at level 1 include various forms of Telepathy.
An other capability that I want to see become more normal from level 1 is phasing thru solid objects. Designers have been wary of it because it might spoil dungeons plans. But I feel Protection from Evil effects (more accurately called Planar Protection) should be able to block phasing, scrying, teleporting, etcetera. A new item, akin to holy water, should be "salt of protection", that can create such Planar Protection effect easily at level 1. So, DMs who need to prevent access to certain rooms in the adventure, can enclose it within a border of protective salt.
So, flight is to become a normal feature if D&D.