I have the Digitrax Zephyr system, with a few upgrades, and I can only say good things about it. From what I've heard the NCE sysem is pretty good, too. So, I don't think you can go wrong either way. The issue comes down to features. I'm sure you could view both operators manuals online and get your own opinion. Again, I'm very happy with my digitrax Zephyr. Now, I did add a few extra cabs, and I've yet to reach max current, but all in all, I think it was a great upgrade from my MRC Command 2000 system.
As for installing decoders, I think I agree with Engineshop. Start out by doing the easy drop-in decoders first. While they might be a bit more expensive initially, their ease of installation will not only get you started faster, it will give you at least some idea of how to get into a loco to hard wire a decoder later. I've installed about 30 decoders (of all types) so far. At this point, there probably isn't a decoder I can't handle. And there are people here who have far more experience than me.