I think everyone has their own perspective as to how their layout should look and how it should be operated and that's one part of what makes this hobby great. After all, these are toy trains and there is no absolute right or wrong - just opinions.
Personally, I dislike having to move engines and rolling stock from a shelf or other storage location to the track and then remove them and put them back after a running session so, from my perspective, I like having a large storage yard with as many sidings as I can fit, within reason, where I can park and move trains onto the layout without having to constantly take them on and off the layout. For me, the ease of being able to switch between trains is the ideal situation.
Plus, although trains on shelves can look good; for me, nothing beats displaying and seeing a train on a track and layout in its "natural" state, especially when you have guests over to see your layout.
Again, just my $.02 and we're only talking about a 1 or 2 siding difference at most, but that's my perspective. Your mileage may vary and no matter what version you choose, it's a well thought out design and I'm sure you'll be happy with the results !
