How to install plugins on a per-site basis on a Multisite network?
As for the install part, no, it's not possible. Installation can only be done in the Network panel. Am not finding an official quote, but I'm pretty sure that this is a no-go. But here a couple of places in the core where we can see it: [1] and [2].
From the e-book Multisite 101, there are this suggestions:
Exclude plugins from appearing in plugins menu for normal user in WordPress multisite.
Provides an interface similar to how the ‘themes’ section looks.
Allows you to manage plugin activation.
I just knew MPM, and with it, you can set 3 states for plugins: hidden, visible and active on blog creation. But it cannot be used to enable plugins on a per-site basis, like WordPress offers as default for Themes.
The current plugin version is displaying a couple of notices: one undefined variable and one deprecated function. But those are minor and easily fixed.
I've also seen that it is prepared to deal with "premium" plugins, using a third-party add-on or plugin. This can be useful for custom tweaks.
None of the plugins in the list has been updated recently, not necessarily bad, but caveat emptor.
I have one plugin that works on the Network screen to show which plugin is active where, as this info is not available in the system.
B/c all of the sites use the same filesystem folder for plugins, I don't think it is possible it install plugins site by site within a multisite. To make you're life easier, I'd take a look at backup buddy or ns cloner. Both of those make it really easy to clone one site to another in multisite. I prefer ns cloner, but that isn't to say I know of anything wrong with backup buddy.
If those don't help and you're comfortable in sql, you can look at copying the row in wp_option_x where option_name = "active_plugins" from site you wish to copy to the new one. That will be a shortcut to activate the plugins on a new site.
Hope that helps.