According to my sources, Flygon and Ferrothorn are roughly equally useful, and Excadrill is much better than both.
Trapinch
Availability: Early-Mid Game, Desert Resort, 5% (Desert)
Stats: Trapinch is very strong, but frail and slow. Once it gets to be Flygon, however, all of it's stats are respectable, with high Speed and Attack.
Typing: Ground is a solid typing, but having some common weaknesses makes it have a hard time. As Vibrava and Flygon, its secondary Dragon-type removes some of them, while it provides a great secondary STAB.
Movepool: Sadly, it can't get Earthquake during the main story unless you keep it as a Trapinch until level 55. Dig or Earth Power serve as decent substitutes, though, and it learns Dragon Claw by level. It gets nice coverage moves like Fire Blast and Rock Slide. You can also use it for Fly.
Major Battles: It does really well against Elesa. It can also do work against Skyla with Rock Slide, while Dragon Claw helps against Drayden. Its Ground-type moves will be helpful against most of Team Plasma.
Ferroseed
Availability: Middle. Ferroseed is a common sight in Chargestone Cave.
Stats: Although the Ferroseed line's high defenses and low Speed are obvious, the Thorn Seed Pokémon is more powerful than it might appear.
Typing: The sturdy Grass/Steel typing means that as long as you keep Ferroseed away from Fire-type moves, it should do fine.
Movepool: Unfortunately for Ferroseed, it's stuck with only Steel-type moves and the weak Pin Missile until evolution, meaning that although it can take hits, it often can't do much damage in return. Ingrain and Iron Defense are good support moves that strengthen Ferroseed's longevity; for example, after a few uses of Iron Defense, even most Fighting-types can't break through Ferroseed. Despite its bad coverage, Ferroseed starts with Gyro Ball, which usually has very high power due to its nonexistent Speed. After it evolves, Ferroseed's bad coverage is remedied when it gets access to Bulldoze.
Major Battles: Ferroseed does okay against the sixth gym, but it can't get past Swanna and Skarmory. It does very well in the two remaining gyms, however, and it completely stops most Plasma grunts as well as Zinzolin's entire team. Even the Champion carries many Pokémon that can't hurt Ferroseed.
Additional Comments: Metal Claw will miss.
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TLDR Flygon has better offensive stats, offensive typing, and coverage moves, while Ferrothorn has evolves earlier and has better defensive typing and a better STAB move. There's also Excadrill, which combines all of these advantages (although its defensive typing is slightly worse than Ferrothorn's). Is there a reason you're not using Excadrill?
