Is it possible to change de color of the scrollbar thumb? here it's light grey over lighter gray, not easy to find it when the gutter is filled with color marks...
No. Colors are hardcoded / theme specific. Try dark Darcula theme (v6 EAP builds).
By "theme" I mean not editor/syntax colors, but GUI colors (previously known as Look&Feel).
You can try it now -- different major versions can run next to each other (IDE wide config/cache files are stored in separate folder -- you just need to backup project settings (.idea subfolder) if you want to work with the project in v5 later).