The Romulan War And Future Guy
It was intended that the main villains of the fifth season would be the Romulans with the idea that it would lead up to the impending Romulan War which would result in the formation of the Federation. Of course, we never got to see that war, which is sort of the Star Trek version of the Clone Wars in Star Wars the big battles that have been often talked about but never yet seen on screen. Part of this would have seen "Future Guy" revealed. Now despite his wibbly wobbly timey wimey form, I always thought he was a Romulan from the very first time I saw him. It's the outline with the shoulder pads. Rick Berman and Brannon Braga have since said that he was "probably going to be a Romulan". However, they have since denied this and claimed it was going to be Archer himself. So who knows. But I think that Coto would have seen sense and wrapped it neatly into the new storyline.
The First Starbase
We've seen a variety of Starbases throughout Starfleet, but of course in the days of the Enterprise series there wasn't any. So one of the ideas that was planned to be included in season five was to see the construction of the first starbase itself. Where exactly this was to be, we're not sure although Starbase 1 was placed in Earth orbit in the JJ Abrams films, but I think that the first Starbase would more sensibly be situated where it could almost act as Babylon 5 particular to act as a neutral territory for humans, Vulcans, Andorians and Tellarites to meet.