Hum both have flaws in some aspects
CS1 - a cast that is too big to make everyone interesting, sadly deep characters and their interactions was the strong point in Sky and Crossbell. Like every first game in a trails saga, very slow story and mainly low stakes events through the game.
CS2 - Someone in the OT once said that the war of the game it's like it's for kids. Because we don't ever see a town being destroyed, people having to flee, almost every NPC is very calm for a freaking civil war, no deaths of important NPCs, no blood, out "third faction" centrism that it's a lie, enemies letting us go and never seriously trying to take our lives... Plus this game is clearly padded a loooot.
If you asked me just after CS2 had been released I would said the sequel is better, but after replaying CS1 and seeing things that were implied or teased that are happening in CS3 elevates the game.
In the end I think CS1 is a game that is aging better with the sequels and the story advancing and CS2 is the opposite.