I lived out of mine for 21 days and 7k miles of camping this summer. You get used to the system, and used to where things go and how to pack it, and some of these issues become...well... non-issues.
The lower bags opening is smaller that objects you might be able to put inside of it, but it is also the lower bag in the system, so think about what will be packed in there, and the order of things you use. The stuff you want quick access to, and use every night that are the first things unpacked, you put in the easy to access places.
The only issue I ever came across trying to pack this, was when I was initially trying to pack it, I had hoped to put a hard sided cooler in there, that did not fit. I ended up going with a soft sided cooler in the main bag that worked. Other than that, I found that fitting clothing for camping and camp meals and things of that nature work well in the lower bag, since I normally don't access that stuff until after camp has been set up. For things of that size and use, the opening is perfect.
Now, I do have one thing that I would change if I built the bag. I actually ran into a twisted-throttle rep while I was in Lassen NP, and mentioned this to him.
The two small side pockets are the larger bag, are useless, they have no purpose. With the hard shell in them, the pocket can not fit anything in it. I can not even put my keys out of my pocket in that area, because it is too small of a pocket. If that pocket articulated out in some way, so it was actually usable that would be perfect. I have tried to find some way to use it, and the only thing I have been able to fit in that spot is a flat key ring style bottle opener. Its a small niggle, but i think you could save money and leave that pocket/zipper off, or just put a little extra material so that it was an actual pocket that you could fit small things in it.