There is no simple reason to run Choice Scarf Palkia over Choice Scarf Garchomp, and vice versa in honesty. They are generally played completely differently, even if you ignore the general special / physical split. Garchomp's Outrage can be annoying at best as it's inviting certain pokemon to just set up all over it, or just deal tons of damage to it (eg. Forretress, Groudon). Oppositely, Palkia can just switch out to a designated counter. Arguably you can just avoid Outrage but then Dragon Claw is nowhere near as threatening.
On top of this, Palkia is far less predictable. Garchomp is generally one of two sets (Choice Scarf and Swords Dance, although arguably Choice Band is in there somewhere). Either way, Garchomp is sticking to the physical side and its counters often double up and counter more than one of its sets. A well played Palkia is much harder to face in my view because it's so unpredictable. Even on a Choice Scarf set, you never know if it's running Aqua Tail / Outrage, or even Focus Punch to catch Blissey off guard.
Garchomp also does not have a strong Surf, Thunder, or Draco Meteor. When you see Garchomp it's generally more obvious what it wants to do as opposed to Palkia.
I also prefer Palkia's typing, but arguably that is only because of the x4 Water-type resistance (Thunder immunity is nice for Garchomp, but most Thunder users also carry Dragon Pulse / Draco Meteor / Ice Beam / a strong Surf or Water Spout).
However, there are plus points to Garchomp, but I won't address them seeing as you were arguing for Garchomp and likely know the plus points of Garchomp already. Palkia and Garchomp tend to need different support in a team, so I personally dislike saying that one is straight up better than the other for the reasons explained above.