Here's the trick, though, is that you shouldn't necessarily be expecting to be able to run pretty much all of your important programs ALL the time. The decision-making and risk analysis/management is part of the game. You can always choose to have all those programs running at once, but the downside is the Response penalty. If you don't want the Response penalty, then you have to manage your risk and choose some programs to not be constantly up. Conceptually, it's not much different than the Street Sam having to pick and choose what 'ware he wants because he doesn't have enough Essence to get it all.
Thusly, what we're going to do for the near future is run this as written in the core book. That'll let me get a handle on what you are and aren't able to do. If, after a few sessions, it's leaning toward "the core rules need modifying" to make the decker work, then we'll almost certainly swap over to the Unwired gear (plus being able to introduce the Unwired gear during play can be a good plot hook). I need to see it in play for myself before I make a final decision on this. I'm not saying no - I'm saying that I need play experience to make a final decision, and the dammed Matrix rules are unintuitive enough that I can't abstract them in my head to tell you one way or another which way I'm leaning.
However, on the "datatrail" thing...yeah, I'm generally not going to worry about that anyway. I always assume that deckers are getting their programs from other Shadowland-types who are removing the copy protection (etc) as a matter of course (or they wrote their own software which didn't have that in the first place). If you manage to get into an Ultraviolet host, they're probably going to be able to track you down anyway, legal software or no. So under "normal" parameters, you won't have to worry about that, and ESPECIALLY not the degradation BS. I don't want to have to track that, and I assume you don't either.