I'm planning to write a Megaman Legends fanfic with Daring Do, but do I start at Legends 1 or 2?

Well I would say 1 as it is the better game... However 2 leaves us with so much potential I mean trapped on another world it is like they did the explanation for you. So ya I would have to say Legends 2.

My personal recommendation would be to have your story take inspiration from the Legends games without feeling like you have to be tied down to one game. For example, you could just as well have the story start out on Kattalox island (or a similar location) and then have them fix the ship up earlier so they can go exploring other islands as well. You could sort of abridge the first game and go into the second game soon afterwards.

Such as... Daring do finds herself on Kattalox island just before the pirates attack. The heroes and villains find themselves fighting over the town while simultaniously exploring the ruins for ancient technology and refractors. However, this awakens Juno who thinks this means that the carbons have become so numerous that they are going to war over resources and starts sending out Reavers to "cull the population" and only summons the giant space weapon if it looks like the reavers on the island aren't enough to solve the problem. Cue people and pirates alike uniting against this new threat and the situation is only resolved once they either defeat Juno (which may or may not be possible since he can download himself into a new body), or if they can solve their differences and convince Juno that they will no longer fight destructive wars with eachother.

Come to think of it, Juno could try wiping out the island with ice as a nod to the Windigos from MLP and maybe tie in with the forbidden island from the start of Legends 2. The Carbon Reinitialization Program could involve summoning a huge storm outside the island to keep it 'quaranteened' and then start freezing everything inside like what people see around the forbidden island. Once Daring Do learns about this, she can make plans to get past the storm and determine why that island was frozen (and apparently kept that way long after the normal reinitialization process would have been carried out).