Hey seiatsu,
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Additionally, how much meter does each charge shot use up.
It depends on the level displayed on your charge shot meter. If it's at LV.1, your plane would use just the green section of your meter. The rest of the meter would be unused. For example, suppose the green section is totally filled and the yellow section is almost totally filled. If you use a charge shot, then you would have a totally filled green section and a yellow section that's a little bit filled. Exactly how much gets used, I don't know.
If your charge shot meter is at LV.2, your plane will use the green and yellow sections, and whatever is left would be unused. And if it's at LV.3, your plane will use the entire meter.
Note that you can't use just a LV.1 charge shot if your meter is already at higher levels. For example, if your meter is at LV.2, you have to use the LV.2 charge shot. So if you would rather, say, use two LV.1 charge shots in quick succession, don't fill the meter to LV.2.
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I know shooting stuff builds meter but is there any method to the rate it builds based on the particular enemy
I don't think the type of enemy has any effect on how fast your charge shot meter builds. Your meter fills the fastest in the green section and slowest in the red section.
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Is bombing discouraged here?
That depends on your goal. If you just want to beat the game, then I encourage you to use your bombs. If you want a high score, then it's discouraged. From all the high scoring replays I've seen, the bomb has been used only for protection, not for any scoring tricks.
By the way, as long is your bomb stock is at 9 and you collect a bomb icon, you'll always get the 10,000-point bonus. Your bomb stock is capped at 9, but the number of times you can get this bonus is uncapped.