Hobbes, you do realize that if you have a Power on in a Background Count, you take the Count's rating as a penalty to any dice-pool affected by the power? Improved Reflexes on means all of your Reaction-based rolls (like Defense tests) will be taking a dive. Your Fingers won't be so Nimble when you're in a Background Count either.
And there's plenty of fluff reason to be a mundane character without 'ware. Personal reasons, health reasons, financial reasons, etc. The list goes on. Just because a person isn't magical, doesn't mean they don't want to replace their eyes with cameras, or stick synthetic weirdness into their body, or have an internal organ replaced with something that has a battery.
On top of that, not everyone can be Awakened. Only 1 in 100 have any iota of magical potential, and it only ends up being around 2,500 in 1,000,000 that have an appreciable Magic score with their minds (relatively) intact.
In the end, there's no thematic reason against making a 'ware-free mundane; there are mechanical consequences to that decision, however. Some are good (no magic or 'ware to get detected, easier on your wallet and your Karma), some are bad (you won't have some of the nifty abilities and your dice-pools will be a bit shorter). In the end, you should play what you want, just make sure to factor in the ramifications of your choice beforehand so you have an idea of what you're getting into.