I think with the speed of a runaway mine train you could have an amazingly themed dark coaster.
I like the idea of having multiple rides share an indoor area.
For anyone that went to American Adventure back when it was stil around, their Runaway Mine Train was themed around a mountain and mines...the ride started off outside doing its usual helixes before entering a cave in the mountain and entering the mines, there were then multiple sections where you would come out of the cave and re enter at a different point.
Now, American Adventures indoor sections were pretty poor, there was no theming and it was just an indoor section with lowered light levels. If there were sparkles of gold on the walls, and animatronic miners, along with theming like buckets of coal/gold, other railways, budgies hanging up, etc you could theme a runaway mine train, log flume and rapids to all intersect the same indoor section and have the whole area themed after a gold rush america type place.
I've seen it done well at other theme parks. Obviously this could be done at Alton Towers but I doubt rides such as the RMT and Rapids would get the money to put theming into their current indoor section.
Would be nice for rides of the future to take it into consideration though.