There are a few sub-quests (for lack of a better term) with choices that can only be determined once. Advancing to new difficulties allows you to make different choices since these are generally flagged per difficulty.
Unfortunately (i guess) this is an older game that isn't going to tell you much. For a blind play, you might as well just finish out normal side solo quests to get an idea of things and then look up guides regarding Soul Eater and Ragol Ring. Doing these on Hard and Very Hard can sorta follow your progression. Note you'll have to talk to every NPC in each quest 1-2 times minimum and some additional digging in a few quests to get details. Even then the story in the game is ... well, eh.
Gov quests generally don't add much to the story; they are more like an attempt by the developers to make multi-mode story. Among other "keep the subs going for as long as possible" goals prior to official shutdown. It might be difficult to find people to do them with as a result.
If you're just interested in leveling and gearing up, doing solo/gov quest progression isn't particularly quick.