There isn't really a "best game", more of a personal preference. Try watching some scoreruns of each to see what you like? Different scoring systems emphasize different techniques-- grazing, planning bombs, spell bonuses, canceling bullets, unfocusing, not dying, etc.
Some scoring systems are more complex than others, PCB and IN in particular. It's not like you have to start with every scoring technique at once, though; you can introduce them gradually. Point item value (PIV) is important in all the games that have PIV systems, so that's a good place to start, along with collecting items to take advantage of that PIV.
In PCB, since you mentioned it, you can start by unfocusing whenever you can, and not shooting bosses during borders-- that, along with collecting point items and good survival, should be enough for over 1 billion Easy/Normal, for instance. Planning your borders for places with the best graze is a major part of PCB scoring, though, so you'd need to start including that sooner or later to continue to improve.
As for what skill level you need to be able to start scoring, you need some decent multitasking ability (to be able to consider scoring mechanics as you play, without randomly dying from lack of attention), something you should have around the level of Extra clears and Hard 1ccs. As well as decent consistency at most of the patterns in whatever difficulty you score. I think you're well over that level already.
