In no particular order:
Use the Mini-Map instead.
Find a Theme that suits your preference.
Modify the [ default | installed ]
theme to suit your preference.
I recently wrote up a post regarding visibility improvements in ST, although it doesn't cover scrollbar settings. ( but it does have some tips for altering mini-map colors )
Two things you can look into are the
scroll_bar settings @ your
sublime-theme file and the
overlay_scroll_bars setting at your
( I mostly use the mini-map viewport, but will occasionaly use the scrollbars for larger files )
( I'll be releasing this as a combined
color scheme after I wrap up some current projects )