1. You note that the browser still powers the apps even though they are 'native'. What sort of performance limitations does this bring up?
. Will the service cost money in the future? as in monthly payments?
Possibly - it's up to PhoneGap, and I'm not sure they're certain of their plans yet, but there's a chance they'll keep a free version. Best try it out now while it's free!
. You also note that only one sound will work at a time. Is this a limitation that will never be fixed or a simple missing feature?
As the r66 changelog notes, it's a hardware limitation. We might be able to work around it with uncompressed WAVs but we'd have to be careful to do that in a way that means nobody can accidentally upload gigantic WAVs to their server that ruins the game download time.