What if the center row was determined by the number of Flooding/Inundation on the field? For example:
1 Flooding = Top/Bottom row and 7th slot flooded
2 Flooding = Top/Bottom row and 6th-7th slot flooded
3 Flooding = Top/Bottom row and 5th-7th slot flooded
4 Flooding = Top/Bottom row and 4th-7th slot flooded
5 Flooding = Top/Bottom row and 3rd-7th slot flooded
6 Flooding = Top/Bottom row and 2nd-7th slot flooded
7+ Flooding = Top/Bottom row and 2nd-7th slot flooded (to prevent Mindgate and Arena/FG decks from flooding the whole field)
Keeping 6 Flooding up at one time isn't exactly easy, plus you'd have to draw them all. If this were to happen then there's the possibility of changing them to stack the way some Shards were, though 1 PA to protect them all may be overpowered.
edit:
After looking at the way creatures are positioned, it may make more sense visually (but be harder to play against) if Flooding worked in this order:
1 = 7th
2 = 7th, 6th
3 = 7th, 6th, 3rd
4 = 7th, 6th, 3rd, 2nd
5 = 7th, 6th, 3rd, 2nd, 4th
6 = 7th, 6th, 3rd, 2nd, 4th, 5th
as creatures are played in this order:
7th - 3rd - 4th - 1st - 5th - 2nd - 6th