Well I'm 6'3", so I have a skewed perception.
My point is this. Say they cast Isaac, who's 5'9". Put him in some combat boots and some lifts, he comes in at 6'0". Now suppose Reeves casts other actors in the 5'9"/5'10" range. Use camera tricks when necessary. Suddenly Isaac's not looking so short, is he?
Let me put this another way. Did you perceive Keaton as being short in the role, or do you think Burton did a good job at making him look tall and foreboding with all the usual tricks? I don't see fans still hung up on his height.
This isn't that difficult. Hell Nolan did it with Hardy in TDKR. Had him standing toe to toe with Bale.