A really good margarita should have exactly three things in it, IMO... tequila, triple sec, and lime juice. That's it. Approximately a 3:1:2 or 2:1:1 ratio is about what I like.
I agree that many store-bought mixes leave something to be desired. With that said, however, getting a somewhat better tequila helps immensely as well, and may well be more the problem. I wouldn't necessarily use a $50+ higher end tequila for mixed drinks, but for ~$30 a bottle you should be able to get a pure blue agave tequila... Hornitos, 1800, Milagro, are a few that come to mind for me.
If you're looking for varieties besides just the typical lime flavor, I can say I've enjoyed replacing triple sec with St Germain (elderflower liqueur), or even blackberry brandy for something completely different.