I recommend Magneton because it has more defenses with Evolution Stone, and gets to ditch Flash Cannon for Magnet Rise, eliminating its Ground weakness. A Timid HP Fire Magneton with 252 EVs in Special Attack and 252 EVs in Speed only has 20 Special Attack points less than a Timid HP Fire Magnezone. The same Magneton has 22 more Speed than a non-Choice Scarfed Timid HP Fire Magnezone. A Modest HP Fire Magneton with 252 EVs in Special Attack and 252 EVs in Speed has 22 more Special Attack than a Timid HP Fire Magnezone, and only 2 less speed than a non-Choice Scarfed Timid HP Fire Magnezone.
Magnezone gets more HP and Choice Scarf, but Magneton gets Magnet Rise and more defenses. You may want to invest in HP for Magneton.
A Timid HP Fire Magneton with Pre-Evolution Stone, with no investment in Defenses, has 339 Def and 264 Sp Def. A Timid HP Fire Magnezone, with no investment in Defenses, has 266 Def and 216 Sp Def.
A Timid HP Fire Magnezone with no investment in HP has 281 HP. 282 if the 4 leftover EVs are invested in HP. A Magneton with these same stats has 241 HP and 242 HP with 4 points of investment. This Magneton needs to invest 160 EVs into HP in order to reach the same in HP as the Magnezone that doesn't invest in HP at all. A Timid Magneton has 60 less Special Attack than a Timid HP Fire Magnezone with 252 Sp. Atk and Speed EVs if it sacrifices Special Attack, and 22 less Speed if it sacrifices that. For a Modest Magneton, the differences are 31 and 41, respectively.
A Magneton that invests 252 EVs in HP has 304 HP.
So maybe you shouldn't invest that much in HP just to meet Magnezone's.
I'd go with Modest for Magneton, unless you're trying to outspeed Scizor.