When Marty goes into the future they should arrive in a future where he went missing (because he's traveling through time). Hence, the whole movie makes absolutely no sense at all.
Not necessarily, you're looking at time and dimensionality in a linear light (ba-dum-dusch!). In all seriousness, by traveling through time he could just be traveling to a parallel dimension (universe?) that has already progressed to a future time.
At the beginning of BTTF2 Marty travels to a possible future. One that would have become the actual future if he hadn't interacted with anybody and then gone straight back to 1985. Doc Brown's plan would have worked too if it weren't for those meddling kids.
When Marty goes into the future they should arrive in a future where he went missing (because he's traveling through time). Hence, the whole movie makes absolutely no sense at all.