A couple of watts is insignificant. The alpine will have better reception though my friend put one in her car and said the recpetion wasnt quite as good as stock but the sound was a lot better. The jvc will be even worse with recpeption. The alpine also has 3 rca outputs which means it should have a sub level and freq.
Personally id take the alpine over jvc any day of the week. Maybe jvc have gotten better though. I heard Eclipse uses a rebadged jvc unit. Or maybe that just how low eclipse has slid. But anyways...