It's not tough to get around..Once you get the MOJO you'll see just how versatile the CTRLR is. It's really a great control.
If you don't like mouse mode on the controller, plug in a real mouse or use a BT mouse. I've used both, and do prefer them to using the CTRLR.
I've not really gotten into Retroarch, yet. I've got it, but since I've actually paid for all the other emulators, I've not really seen a point in using it.
ALSO: Lots of people are switching to Nostalgia.NES over some of the more popular ones..In my opinion, the .EMU are better overall....I mean how important is a FF option? I wish I'd saved my $1.50.
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