Honestly just scrap everything after the last Tartaros chapter and go in a completely different direction for optimal results if I'm being honest. He started making mistakes right away bringing Natsu back immediately and just a lot stronger. If he'd been missing for ages, that'd have been something - could then have had a reason for it, was Zeref involved, the Avatar Cult, Acnologia even? Build the story from there.
Have Lucy on her own for a while, and finally reach the point where she decides she's going to go see her friends, not just wait for Natsu to whisk her off on another adventure. Show Lucy's grown as a character in self confidence since the start, not ruin all of her development with some lame 'what if they don't like me' self doubt. Have happy join her and tell her even he doesn't know where Natsu is - up the suspense.
Have Lucy go to Other guilds to look for people/ clues to where they are, have her interacting with new characters, making more friends, interesting exchanges - she could find Laxus/ the Thunder God Tribe first and go with them for a change, she could find Cana in a pub somewhere and restart their pairing, Wendy even, just something a little bit different!
Start meeting up with other guild members and exchanging stories with them - what have they been doing, surely they know things/ have ideas of where to look. Continue on, encounter some bad guys who end up offering the next clue, or find Brandish who is secretly on a scouting mission for whoever, or doing anything else. Have her recognise Lucy from the start. None of this is difficult to come up with and would have been a lot more interesting/ varied than just the same old same old we ended up getting.
)
