The downsides is that its probably the most annoying menu system in a point and shoot mirrorless camera - Sony aims the NEX range to people who want to point and shoot and then later want to use manual and creative functions as they get better at it.
As a NEX user, I can't really disagree with this - the menu system is just a mess in my opinion. However, I wanted to point out that at least the menu system can be largely avoided on the NEX, as there are a large number of programmable buttons available, so that up to 9 functions can be routed to direct external button control helping avoid ever going in the menus in the first place.
Also, people forget that for the NEX and the Samsung ranges you have to purchase a seperate flash. (please correct me on this as 2 friends have a NEX and a NX1000 and they both dont have flashes in the box when I saw them with it in December.)
I'm not 100% on the Samsung, however, the NEX cameras should all come with a flash unit in the box - it's a small screw-on type that fits to the top, and can be left on as it's quite small - or left off if you're not likely to use it or need it. The flash is standard issue with the NEXes.
Otherwise, I'll just add that there are no 'best' mirrorless cameras or systems - each has advantages and disadvantages, and different people have different needs or likes that help guide them to the system that will work best for their needs. So no worries - just check them out, read about the features, and then pick the one that fits you best.
Sony DSLR-A580 / Sony 18-250mm / Minolta 50mm F1.7 / Sigma 30mm F1.4 / Tamron 10-24mm / Tamron 150-600mm / Tamron 90mm F2.8 macro / Minolta 300mm F4 APO
Sony A6000 / 18-55mm F3.5-5.6 / 55-210mm F4-6.3 / 10-18mm F4 / 35mm F1.8 / 16mm F2.8 / via manual adapter, lots of Pentax K mount, Konica K/AR mount, and Leica M mount manual lenses