Personally, the only thing I would have changed from this arc is the number of Spriggan. Even if Hiro had the time and the right pace to write this arc he would have failed anyway because he put too many unnecessary villains in this arc and the fights would have been missed anyway. So you might as well keep the useful Spriggans who have something to contribute to the story (August Irene God Serena Brandish Invel Ajeel). For Acnologia and Zeref I don't know what we could have changed. They were far too powerful to lose in a fair fight. With hindsight I don't blame the author for having poorly managed their ending. As
@Ebony Maw said he managed his work well despite the pressure he had and the lack of time, and In his place I would have also lost my temper.
Reduce the Spriggans, and sort a couple of ill defined things out. Firstly Zeref's actual aim/ motive for the invasion? Yes to obtain Fairy Heart, but I'm still not entirely clear on what he aimed to do with it... if it was take the fight to Ankhseram and end his curse with the virtually unlimited power of FH, that's a tangible goal at least. Secondly I really don't think it worked as a
war arc with zero set up on Alvarez, Alakitasia, or international diplomacy/ military matters in general throughout FT. We just
barely glimpse Fiore's government, and it's relationship to the Magic Council is poorly defined. If it was building to a war that's what he should've been sprinkling in all the way through the series.
Better would be Zeref gathered some Human mages (say 5/6 of the Spriggans) and had a small army of new etherious around him, and planned to attack Fairy Tail for Fairy Heart in particular. Recruiting Natsu as END for his second in command could fit into his plan, to at least do something with that plot point, even if it is the most basic obvious thing going. Each of the Spriggan fights would've worked better as 2v1s against Fairy Tail pairs - I actually quite liked what he tried to do with Lucy & Natsu vs Jacob, and Wendy & Erza vs Irene, in principal at least. Lets them live up to their hype a bit at least. The rest of the spriggans could have been re-worked into the etherious enemies to give the tertiary characters some decent fights.
The only thing I'm really stumped on is what to do with Acno, he doesn't fit in here particularly well as there's already a lot going on.
Really needed his own arc tbh. Probably could've re-worked the Future Rogue and Eclipse Dragon part of the GMG and moved it a bit later (Rogue comes through during the games, but doesn't make his move until later, after Tartaros or so?).