Micoscope could word very well because in the stories there are often some long lost civilasations to explore and stuff. Or at least you sens something odd but can not figure it out.
Well, it depends on how complex you want the time manipulation mechanic to be. A simple set of action points that let you undo a mistake and roll again with a large bonus (after all, you know what you did wrong) would work as a basic beginning. Perhaps you could also speed these sand baubles to get multiple actions or move at five times normal speed to represent the rest of the world slowing down. Or it could be a system based on action points, and each bit of bonus time gives you a bunch of extra AP.
To keep an easy idea - you have a four point action pool, and a two point reaction pool. Reaction lets you move or dodge, while action lets you swing shoot, and so forth. An attack takes only one point to activate, but spending extra AP lets you aim or add special effects to each hit. I'd probably say something like base skill is 20% to hit (1 AP) and then multiplied by AP (so two AP = 40, 3 =60 etc) so as your skill gets better, the bonus goes up quite a bit.
More advanced time manipulation that lets you interact with past selves, age enemies to dust, or restore crumbling ruins would be a bit more complex to handle mechanically, and might just need to be a part of the scenario itself.
Games of imagination are never truly done. Yet tomorrow we shall start another one.
I like the idea. Maybe you could also use sandpoints to look forward or backwards in time to create a plothook. You could use a normal d6 for the game: you need a 6 and every point of sand adds a point to your result. Rewinding time does not give you a bonus but you cann roll again (and again and again). But what happens when a partymember rewinds time? Are the other memers rewinded as well? Are they aware of the progress?
Third possibility: The characters are linked. If one manipulates time it affects all characters. And if they combine their power they can do very nasty stuff but are out of sand very soon.
Or there is only one character, but with a split personality, like in the third game.
Or you make an "A strange charm" ripoff. Everyone has a role, e.g. antagonist and in every scene he is the antagonist no matter who the antagonist is in that scene.