The Homing Attack was honestly the next evolutionary step in the Sonic 2D gameplay. There really isn't much else a grounded hero like Sonic can do beyond using the elements, and that turns your IP into a gimmick.
The Homing Attack is an auto-enemy lock attack that works well in high speed situations and helps in figuring out enemy weakspots and boss strategy as well as keeping the character moving. To have the elemental shields was fine; Fire provided protection and a speed boost, Elec attracted Rings, and Water gave a higher second jump and protected against 5-4-3-2-1-0-bwaaaaaah... But assigning a specific element or tool as a semi-permanent part of the character has provided less-than-admirable sales and stories in such games as ShTH (gun), Secret Rings/Rush (fire), Black Knight (sword), etc.
Mario was also susceptible to the same: the first Mario and Luigi game gave Mario the fire element and Luigi the electric element, but did not contribute to the entire series or the Smash games. Luigi's manipulation of electricity was indeed a gimmick and not considered nor useful in future installments of the main Mario Bros. series or even the Smash games, wherein he returned to fire. The Poltergust and the FLUDD have all but disappeared in the main lines (although the FLUDD did make a brief return in SSBB). Mario and Luigi do don elemental powers such as fire and ice, but only as suits, temporary uses.
Sonic, on the other hand, keeps gravitating to one gimmick after the other; again, the result of overpowering a largely grounded, non-armed lead by every other character. The Homing Attack is now an extra physical ability that the athletic hedgehog has, no real issue there. And even back in the day, we were headed toward that route. Sonic 3D Blast introduced the Gold Shield which gave Sonic the Homing Attack, and then we see it as an ingrained ability in Sonic Adventure. In a similar fashion, Mario gets a slight horizontal carry by shaking the Wiimote in NSMBWii; I believe Luma's granted power has taken some small hold in Mario by upping his jumping ability slightly, even if it's not a full vertical carry.
Long story short: It was going to happen anyway, and as long as they don't mess up the physics, the series is better for it.