Woocommerce all the way, due to an extensive library of plugins, customisation options, ability to move to whichever server you need to.
Hmm - we just migrated off Magento as we had to upgrade to v2 (which essentially required a full recode) so we undertook a full review of our £3.5m pA turnover online operation. We decided against upgrading to Magento v2 for three main reasons: (1) it seems prone to being hacked and having malware inserted; (2) customising seemed to be harder/more expensive than on competitor platforms; and (3) it was recently sold to Adobe who are not shy about being very aggressive on price increases/licence fee increases. After doing a full review we rewrote the site to sit on BigCommerce. We are very happy with the results.
Just my two thoughts, I think woocommerce is a good solution for people who know what they're doing from a website perspective. But I think shopify is appealing and works better for those that just want the shop done. I have a woocommerce store and currently have about 6,000 products on it. It works great, loads fine. I have found that the problem with woocommerce sometimes stems with the host (was on Hostgator and it was terrible). Agree with previous posters about plugins clogging up the system. It's true, just because its free doesnt meant it's good! Be smart about it.