I'd recommend the Helix Fossil over the Dome Fossil. This is going to be a long explanation, so bear with me.
Both the Helix Fossil and Dome Fossil can be revived to form Omastar and Kabutops respectively, which are Rock and Water type. As you should know, move types that match with the Pokemon type get a 50% power boost (known as STAB, Same-Type Attack Bonus). For 3rd Generation Pokemon Games, Rock type moves' damage are calculated with Attack, while Water type attacks are calculated with Special Attack. Water type moves shouldn't be taught to Kabutops, as Kabutops' stats focuses on attack. There aren't any powerful Rock-type attacks that Kabutops can learn in FireRed. Because Omastar's stronger offense is Special Attack, it shouldearn Surf and Hydro Pump, both of which are quite strong Special attacks that Omastar can learn.
If you're looking to migrate Pokemon to 4th Generation Games, then either can be chosen, as 4th Generation introduced a powerful Rock-type attack, Stone Edge and different Battle mechanics.
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If you choose the Helix Fossil it can be revived into an omanyte. The Dome Fossil can be revived into a kabuto. I suggest you pick based on what pokemon you like better.
The Pokémon Omanyte is in the helix fossil.
When you clone the helix fossil later on in the game, the Helix Fossil can be regenerated into an Omanyte. The Dome fossil can be regenerated into a Kabuto.
tThe Helix Fossil evolves int Omanyte
Dome Fossil = Kabuto (Lv 40, evolves to Kabutops) Helix Fossil = Omanyte (Lv 40, evolves to Omastar) Old Amber = Aerodactyl